From 772a9a35837308d7284ec3afc3b578e271bdf45b Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Tue, 5 Aug 2025 10:33:33 -0400 Subject: [PATCH 01/13] Add files via upload --- 06_imputation/correlation_workflow.qmd | 462 ++ 06_imputation/minimal_magic_setup.sh | 77 + 06_imputation/renv.lock | 7792 ++++++++++++++++++++++++ 3 files changed, 8331 insertions(+) create mode 100644 06_imputation/correlation_workflow.qmd create mode 100644 06_imputation/minimal_magic_setup.sh create mode 100644 06_imputation/renv.lock diff --git a/06_imputation/correlation_workflow.qmd b/06_imputation/correlation_workflow.qmd new file mode 100644 index 0000000..89edb7b --- /dev/null +++ b/06_imputation/correlation_workflow.qmd @@ -0,0 +1,462 @@ +--- +title: "co-expression with imputation" +author: "Harvard Chan Bioinformatics Core" +date: "`r Sys.Date()`" +format: + html: + number-sections: false + default-image-extension: svg + lightbox: true + callout-icon: false + format-links: true + toc: true + theme: sandstone + echo: true + eval: true + message: false + warning: false + code-copy: true + code-overflow: wrap + code-fold: true + code-line-numbers: true + embed-resources: true + standalone: true + html-math-method: katex + grid: + sidebar-width: 250px + body-width: 900px + margin-width: 300px + comments: + hypothesis: true +params: + project_file: ../information.R + seurat_obj: "https://github.com/bcbio/bcbioR-test-data/raw/refs/heads/main/singlecell/tiny.rds" + group_column: "integrated_snn_res.0.4" + path_outs: "./test_out" + magic_condaEnv: "magic_env" +knitr: + opts_chunk: + fig-align: "center" + echo: true + cache: false + error: true + highlight: true + message: false + prompt: false + tidy: false + warning: false +--- + +```{r library-load} +#| cache: false +#| message: false +#| echo: false +library(tidyverse) +library(knitr) +library(glue) +library(Seurat) + +library(pheatmap) +library(gridExtra) +library(RColorBrewer) +library(viridis) + +library(CSCORE) +library(SAVER) +library(Rmagic) + +invisible(list2env(params, environment())) +source(project_file) +reticulate::use_condaenv(magic_condaEnv, required = T) + +# Create output directory if it doesn't exist +if (!dir.exists(path_outs)) { + dir.create(path_outs, recursive = TRUE) + cat("Created output directory:", path_outs, "\n") +} + +inputRead <- function(f) { + if (sum(endsWith(f, c("rds", "RDS"))) > 0) { + if (R.utils::isUrl(f)) { + f <- url(f) + } + return(readRDS(f)) + } else if (sum(endsWith(f, c("qs", "QS"))) > 0) { + if (R.utils::isUrl(f)) { + f <- url(f) + } + return(qread(f)) + } else { + print("Check file extension and choose appropriate functions!") + } +} +``` + +```{r report-setup} +#| echo: false +ggplot2::theme_set(theme_light(base_size = 11)) +``` + + +```{r filter-parameters} +# Filtration parameters +filter_gene <- FALSE +min_exp <- 0.2 +min_cells <- 40 +min_perc <- 0.2 +``` + +This report intends to both calculate correlations of gene of interests and also compares how imputation changes those values. + +Throughout this report, we assess two main ways of calculating gene correlations scores (**`Spearman` and `CS-CORE`**). + +We further assessed two ways of imputating gene expression values: MAGIC and SAVER. + +More details about the method can be found in the section **Method description**. + +# Overview of project + +- Path seurat: `r seurat_obj` +- Metadata column with cell group label: `r group_column` +- Filter genes based on expression and frequency: `r filter_gene` + +List of all gene of interests: + +```{r gene-of-interests} +corr_genes_all <- c( + "COL1A1", "COL1A2", "DCN", + "EBF2", "IL33", "PRX", "LY6G6C" +) +DT::datatable(data.frame(gene = corr_genes_all)) +``` + +Starting off with `r length(corr_genes_all)` genes of interest. + +# Load seurat object + +```{r seurat-loadin} +seurat <- inputRead(seurat_obj) +Idents(seurat) <- group_column +seurat[["SCT"]] <- NULL +raw_rna <- GetAssayData(object = seurat[["RNA"]], layer = "counts") +genes.use <- rowSums(raw_rna) > 0 +genes.use <- names(genes.use[genes.use]) +seurat <- seurat[genes.use, ] +n_cells <- ncol(seurat) +``` + +From the genes that were supplied, removing any that are not expressed in this dataset. + +```{r only-present} +corr_genes <- corr_genes_all[corr_genes_all %in% genes.use] +``` + +Next we look at the basic distribution of remaining genes of interest in terms of expression and number of cells they are expressed in. + +These are the following filtration metrics that are set: + +- Average expression < `r min_exp` +- Number of cells expressed in > `r min_cells` +- Percentage of cells expressed in > `r min_perc` + +Filtration parameter was set to `r filter_gene`. If FALSE, no further filtration will be done at this step. + +```{r filtered-gene} +data_rna <- FetchData(seurat[["RNA"]], vars = corr_genes) + +# Number of cells a gene is expressed in +num_cells <- colSums(data_rna > 0) +# Percentage of cells a gene is expressed in +perc_cells <- num_cells / ncol(seurat) +# Average expression of a gene +avg_expression <- colMeans(data_rna) + +df_genes <- data.frame(num_cells, perc_cells, avg_expression) +df_genes <- df_genes %>% + mutate(filter = !((perc_cells > min_perc) & + (num_cells > min_cells) & + (avg_expression > min_exp))) +df_genes$gene <- row.names(df_genes) +df_genes <- df_genes %>% arrange(desc(avg_expression), desc(perc_cells)) +df_genes %>% + select(-gene) %>% + magrittr::set_colnames(c( + "N_Cell_Expressed", "Perc_Cell_Expressed", + "Avg_Expression", "Filter" + )) %>% + DT::datatable() %>% + DT::formatRound(columns = c("Perc_Cell_Expressed", "Avg_Expression"), digits = 3) +``` + +```{r visualize-filter} +#| fig-width: 6 +df_genes %>% + ggplot(aes(x = perc_cells, y = avg_expression, color = filter)) + + geom_point(size = rel(3)) + + scale_color_manual(values = c("black", "darkred")) + + theme_minimal() + + labs(x = "Percent of cells expressing the gene", y = "Average expression") +``` + +```{r remain-gene} +if (filter_gene == TRUE) { + corr_genes <- (df_genes %>% subset(filter == FALSE))$gene +} +``` + +`r length(corr_genes)` genes of interest remaining. + +# Imputation and normalization + +We compare three alternative methods of estimating expression levels to log normalization and assess their ability to account for dropout. + +1. `SCTransform` (raw counts -> normalized counts) +2. `MAGIC` (raw counts -> imputed, normalized counts) +3. `SAVER` (raw counts -> imputed, normalized counts) + +```{r imputation} +# Store output so we don't have to re-run imputation each time +filename <- glue("{path_outs}/imputed.RDS") +if (!file.exists(filename)) { + # Get raw counts + raw_rna <- LayerData(seurat, assay = "RNA", layer = "counts") + + # SCT + # Re-run SCT on subset data + seurat <- SCTransform(seurat, return.only.var.genes = FALSE, min_cells = 1) + + # Creating new seurat object for genes of interest only + data_raw <- FetchData(seurat, assay = "RNA", layer = "counts", vars = corr_genes) + data_rna <- FetchData(seurat, assay = "RNA", layer = "data", vars = corr_genes) + data_sct <- FetchData(seurat, assay = "SCT", layer = "data", vars = corr_genes) + + seurat_imputed <- CreateSeuratObject( + counts = t(data_raw), + data = t(data_rna), + meta.data = seurat@meta.data + ) + seurat_imputed[["SCT"]] <- CreateAssayObject(data = t(data_sct)) + seurat_imputed[["RAW"]] <- CreateAssayObject(counts = raw_rna) + + # Delete the original seurat object to save memory + rm(seurat) + + data_magic <- magic(t(raw_rna), genes = corr_genes)$result + seurat_imputed[["MAGIC"]] <- CreateAssayObject(data = t(data_magic)) + + # SAVER + # Generate SAVER predictions for those genes + genes.ind <- which(rownames(raw_rna) %in% corr_genes) + data_saver <- saver(raw_rna, + pred.genes = genes.ind, + pred.genes.only = TRUE, + estimates.only = TRUE, + ncores = parallel::detectCores() - 2 + ) + + seurat_imputed[["SAVER"]] <- CreateAssayObject(data = data_saver) + + saveRDS(seurat_imputed, filename) +} + +seurat_imputed <- readRDS(filename) +``` + +## Average expression for each method + +```{r avg-expr} +#| fig-width: 6 +assays <- c("RNA", "SCT", "MAGIC", "SAVER") + +df_avg <- data.frame(gene = corr_genes) +for (assay in assays) { + data <- GetAssayData(object = seurat_imputed[[assay]], layer = "data") + avg <- data.frame(rowMeans(data)) + colnames(avg) <- assay + avg$gene <- row.names(avg) + df_avg <- left_join(df_avg, avg, by = "gene") +} + +pheatmap(df_avg %>% column_to_rownames(var = "gene"), + scale = "column", + cluster_col = TRUE, cluster_row = TRUE, + show_rownames = TRUE, + angle_col = 0, color = inferno(10) +) +``` + +# Correlation Estimates + +We have a few different ways to compute correlation scores with their associated p-values: + +1. `Spearman` correlation + - `SCTransform` counts -> spearman correlation matrix + - `MAGIC` imputed -> spearman correlation matrix + - `SAVER` imputed -> spearman correlation matrix +2. `CS-CORE` + - Raw RNA counts -> co-expression matrix + +```{r correlations} +# Store output so we don't have to re-run correlation each time +filename <- glue("{path_outs}/corr.csv") + +if (!file.exists(filename)) { + # Compute spearman correlation for each method (except CS-CORE which is run later) + # Unique combination of each gene pair + genes_comb <- data.frame(t(combn(corr_genes, 2))) + n_comb <- nrow(genes_comb) + + # Create dataframe with correlation and p-values scores + df_corr <- genes_comb %>% rename("Var1" = X1, "Var2" = X2) + df_corr[assays] <- NA + df_p_val <- df_corr + + for (idx in 1:n_comb) { + if (idx %% 200 == 0) { + print(glue("{idx}/{n_comb} correlations computed.")) + } + + # Name of genes to run correlation on + gene_1 <- genes_comb[idx, 1] + gene_2 <- genes_comb[idx, 2] + + for (assay_ in assays) { + gene_exp <- t(seurat_imputed[[assay_]]$data[c(gene_1, gene_2), ]) %>% + as.data.frame() + + if (all(gene_exp[[gene_1]] == 0) | all(gene_exp[[gene_2]] == 0)) { + corr_val <- 0.0 + p_val <- 1.0 + } else { + # Calculate spearman correlation and p-value otherwise + tmp <- cor.test(gene_exp[[gene_1]], gene_exp[[gene_2]], + method = "spearman", exact = FALSE + ) + corr_val <- as.numeric(unname(tmp$estimate)) + p_val <- as.numeric(tmp$p.value) + } + + # Store correlation and p-values + df_corr[idx, assay_] <- corr_val + df_p_val[idx, assay_] <- p_val + } + } + + # Run CS-CORE + DefaultAssay(seurat_imputed) <- "RAW" + CSCORE_result <- CSCORE(seurat_imputed, genes = corr_genes) + + # Store CS-CORE results + tmp <- reshape2::melt(as.matrix(CSCORE_result$est)) %>% rename(CSCORE = value) + df_corr <- left_join(df_corr, tmp) + tmp <- reshape2::melt(as.matrix(CSCORE_result$p_value)) %>% rename(CSCORE = value) + df_p_val <- left_join(df_p_val, tmp) + + # Save output + write.csv(df_corr, filename) + write.csv(df_p_val, glue("{path_outs}/p_corr.csv")) +} + +df_corr <- read.csv(filename, row.names = 1) +df_p_val <- read.csv(glue("{path_outs}/p_corr.csv"), row.names = 1) +``` + +## Heatmap of correlation estimates + +Showing the patterns of correlation for each method. The x-axis and y-axis are the genes of interest with the corresponding correlation value for the pair as the value. Keep in mind that this is symmetric matrix. + +```{r visualize-cors} +#| fig-width: 7 +methods <- c("RNA", "SCT", "MAGIC", "SAVER", "CSCORE") + +cor_List <- purrr::map(methods, \(method){ + corr <- df_corr[c("Var1", "Var2", method)] + corr_cp <- corr %>% rename(Var1 = Var2, Var2 = Var1) + corr <- rbind(corr, corr_cp) + mtx <- reshape2::dcast(corr, Var2 ~ Var1) %>% column_to_rownames("Var2") + + # Set the diagonal values: Correlation = 1, p-value = 1 + mtx <- as.matrix(mtx) + diag(mtx) <- 1 + + breaks <- seq(-1, 1, by = 0.1) + show_legend <- F + if (method == "CSCORE") { + show_legend <- T + } + p <- pheatmap(mtx, + color = inferno(10), + show_rownames = FALSE, + show_colnames = FALSE, + breaks = breaks, + main = method, + silent = T, + legend = show_legend, + fontsize = rel(8) + ) + return(p[[4]]) +}) + +cor_comb <- grid.arrange(grobs = cor_List, nrow = 2, ncol = 3) +plot(cor_comb) +``` + +# Compare correlation estimates across methods + +Comparing the correlation scores for each gene pair for MAGIC, SAVER, and CS-CORE. + +In these scatterplots, the gene-pairs that are colored red have different results for significance. + +```{r cor-compare} +#| fig-width: 3 +#| fig-height: 8 +methods <- c("MAGIC", "SAVER", "CSCORE") +methods_comb <- data.frame(t(combn(methods, 2))) +plot_list <- list() + +for (idx in 1:nrow(methods_comb)) { + method_1 <- methods_comb[idx, 2] + method_2 <- methods_comb[idx, 1] + + corr <- df_corr[c("Var1", "Var2", method_1, method_2)] + p_val <- df_p_val[, c("Var1", "Var2", method_1, method_2)] + corr$sig_1 <- p_val[[method_1]] + corr$sig_2 <- p_val[[method_2]] + + corr <- corr %>% mutate(sig = (sig_1 < 0.5) & (sig_2 < 0.05)) + + p <- ggplot(corr) + + geom_point(aes( + x = get(method_1), y = get(method_2), + color = sig + ), size = rel(3)) + + theme_bw() + + NoLegend() + + scale_color_manual(values = c("FALSE" = "#9D0208", "TRUE" = "black")) + + labs(x = method_1, y = method_2, title = paste(method_1, "vs", method_2)) + + theme(plot.title = element_text(size = rel(1.5))) + + ylim(-1, 1) + + xlim(-1, 1) + + geom_abline(slope = 1, intercept = 0, color = "#63bff0") + + plot_list[[idx]] <- ggplotGrob(p) +} + +grid.arrange(grobs = plot_list, nrow = 3) +``` + +# Method description + +[`CS-CORE`](https://github.com/ChangSuBiostats/CS-CORE) is a R package for cell-type-specific co-expression inference from single cell RNA-sequencing data. It provides an implementation for the statistical method CS-CORE proposed in this [paper](https://www.nature.com/articles/s41467-023-40503-7). + +[`MAGIC`](https://github.com/KrishnaswamyLab/MAGIC) is an algorithm for denoising high-dimensional data most commonly applied to single-cell RNA sequencing data. MAGIC learns the manifold data, using the resultant graph to smooth the features and restore the structure of the data. + +[`SAVER`](https://github.com/mohuangx/SAVER) implements a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data. + +# R session + +List and version of tools used for the QC report generation. + +```{r} +sessionInfo() +``` diff --git a/06_imputation/minimal_magic_setup.sh b/06_imputation/minimal_magic_setup.sh new file mode 100644 index 0000000..4c0d50d --- /dev/null +++ b/06_imputation/minimal_magic_setup.sh @@ -0,0 +1,77 @@ +#!/bin/bash + +# Minimal MAGIC Setup - Just the essentials +# This installs only what's absolutely needed for MAGIC to work + +echo "=== Minimal MAGIC Setup ===" + +# Navigate to 06_imputation directory +cd "06_imputation" + +# Step 1: Remove existing environment if it exists and create fresh one +echo "Creating fresh minimal conda environment..." +conda env remove -n magic_env -y 2>/dev/null || true +conda create -n magic_env python=3.9 -y + +# Activate environment +source "$(conda info --base)/etc/profile.d/conda.sh" +conda activate magic_env + +# Step 2: Install compatible packages from conda-forge (avoids binary compatibility issues) +echo "Installing compatible packages from conda-forge..." +conda install -y -c conda-forge numpy=1.24.3 pandas=2.0.3 scipy matplotlib + +# Step 3: Install MAGIC dependencies via conda/pip carefully +echo "Installing MAGIC dependencies..." +pip install scprep future tasklogger graphtools + +# Step 4: Install MAGIC package directly +echo "Installing MAGIC package..." +cd MAGIC/python +pip install . +cd ../.. + +# Step 5: Test MAGIC (with error handling) +echo "Testing MAGIC..." +python -c " +try: + import magic + print('✓ MAGIC version:', magic.__version__) + print('✓ MAGIC import successful!') +except Exception as e: + print('✗ MAGIC import failed:', e) + exit(1) +" + +# Step 5: Install R MAGIC package +echo "Installing R MAGIC package..." +R --slave << 'EOF' +if (file.exists("renv/activate.R")) { + source("renv/activate.R") +} +install.packages("./MAGIC/Rmagic", repos = NULL, type = "source") +library(Rmagic) +cat("✓ R MAGIC installed and loaded\n") +renv::snapshot() +EOF + +# Step 6: Create minimal R setup +cat > "minimal_magic_setup.R" << 'EOF' +# Minimal MAGIC Setup for R +reticulate::use_condaenv("magic_env", required = TRUE) +library(Rmagic) +cat("✓ Minimal MAGIC environment ready\n") +EOF + +# Update .Rprofile +echo "" >> .Rprofile +echo "# Minimal MAGIC Setup" >> .Rprofile +echo "source('minimal_magic_setup.R')" >> .Rprofile + +echo "" +echo "=== Minimal Setup Complete! ===" +echo "To use MAGIC:" +echo "1. conda activate magic_env" +echo "2. Start R in this directory" +echo "" +echo "Test with: python -c 'import magic; print(magic.__version__)'" diff --git a/06_imputation/renv.lock b/06_imputation/renv.lock new file mode 100644 index 0000000..a3a5c8f --- /dev/null +++ b/06_imputation/renv.lock @@ -0,0 +1,7792 @@ +{ + "R": { + "Version": "4.5.0", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://packagemanager.posit.co/cran/latest" + } + ] + }, + "Packages": { + "BH": { + "Package": "BH", + "Version": "1.87.0-1", + "Source": "Repository", + "Type": "Package", + "Title": "Boost C++ Header Files", + "Date": "2024-12-17", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"John W.\", \"Emerson\", role = \"aut\"), person(\"Michael J.\", \"Kane\", role = \"aut\", comment = c(ORCID = \"0000-0003-1899-6662\")))", + "Description": "Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most useful subset of Boost libraries for template use among CRAN packages. By placing these libraries in this package, we offer a more efficient distribution system for CRAN as replication of this code in the sources of other packages is avoided. 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Kane [aut] ()", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "CSCORE": { + "Package": "CSCORE", + "Version": "1.0.1", + "Source": "GitHub", + "Title": "Cell-type-specific co-expression inference from single cell RNA-sequencing data", + "Authors@R": "c( person(\"Chang\", \"Su\", , \"chang.su@emory.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-8704-1512\")), person(\"Zichun\", \"Xu\", , \"zichun.xu@yale.edu\", role = c(\"aut\"), comment = c(ORCID = \"0000-0002-4001-0321\")), person(\"Xinning\", \"Shan\", , \"xinning.shan@yale.edu\", role = c(\"aut\"), comment = c(ORCID = \"0000-0001-6270-0094\")) )", + "Description": "This R package provides an implementation for the statistical method CS-CORE that estimates and tests cell-type-speicific co-expression networks using single cell RNA sequencing data.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Roxygen": "list(markdown = TRUE)", + "RoxygenNote": "7.3.2", + "Imports": [ + "stats", + "Rcpp" + ], + "LinkingTo": [ + "Rcpp", + "RcppArmadillo" + ], + "Depends": [ + "R (>= 2.10)" + ], + "LazyData": "true", + "Suggests": [ + "knitr", + "rmarkdown", + "MASS", + "Seurat", + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "VignetteBuilder": "knitr", + "URL": "https://changsubiostats.github.io/CS-CORE/", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteRepo": "CS-CORE", + "RemoteUsername": "ChangSuBiostats", + "RemoteRef": "HEAD", + "RemoteSha": "ba63749883bcb55c3d62bdb516e71e537def1afc", + "NeedsCompilation": "yes", + "Author": "Chang Su [aut, cre] (ORCID: ), Zichun Xu [aut] (ORCID: ), Xinning Shan [aut] (ORCID: )", + "Maintainer": "Chang Su " + }, + "DBI": { + "Package": "DBI", + "Version": "1.2.3", + "Source": "Repository", + "Title": "R Database Interface", + "Date": "2024-06-02", + "Authors@R": "c( person(\"R Special Interest Group on Databases (R-SIG-DB)\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\") )", + "Description": "A database interface definition for communication between R and relational database management systems. 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See file COPYRIGHT for details\") )", + "Description": "Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and 'bd' as well as 'kd' trees. The distance is computed using the L2 (Euclidean) metric. Please see package 'RANN.L1' for the same functionality using the L1 (Manhattan, taxicab) metric.", + "License": "GPL (>= 3)", + "URL": "https://github.com/jefferislab/RANN, https://jefferislab.github.io/RANN/", + "BugReports": "https://github.com/jefferislab/RANN/issues", + "Suggests": [ + "testthat" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Gregory Jefferis [aut, cre] (), Samuel E. Kemp [aut], Kirill Müller [ctb] (), Sunil Arya [aut, cph] (), David Mount [aut, cph] (), University of Maryland [cph] (ANN library is copyright University of Maryland and Sunil Arya and David Mount. 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Despite its flexibility, ROCR is easy to use, with only three commands and reasonable default values for all optional parameters.", + "Encoding": "UTF-8", + "License": "GPL (>= 2)", + "NeedsCompilation": "no", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "methods", + "graphics", + "grDevices", + "gplots", + "stats" + ], + "Suggests": [ + "testthat", + "knitr", + "rmarkdown" + ], + "URL": "http://ipa-tys.github.io/ROCR/", + "BugReports": "https://github.com/ipa-tys/ROCR/issues", + "RoxygenNote": "7.1.0", + "VignetteBuilder": "knitr", + "Author": "Tobias Sing [aut], Oliver Sander [aut], Niko Beerenwinkel [aut], Thomas Lengauer [aut], Thomas Unterthiner [ctb], Felix G.M. Ernst [cre] ()", + "Maintainer": "Felix G.M. 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The matrix to be computed on can be dense, sparse, or in the form of an operator defined by the user.", + "License": "MPL (>= 2)", + "URL": "https://github.com/yixuan/RSpectra", + "BugReports": "https://github.com/yixuan/RSpectra/issues", + "Depends": [ + "R (>= 3.0.2)" + ], + "Imports": [ + "Matrix (>= 1.1-0)", + "Rcpp (>= 0.11.5)" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "prettydoc" + ], + "LinkingTo": [ + "Rcpp", + "RcppEigen (>= 0.3.3.3.0)" + ], + "VignetteBuilder": "knitr, rmarkdown", + "RoxygenNote": "7.1.2", + "NeedsCompilation": "yes", + "Author": "Yixuan Qiu [aut, cre], Jiali Mei [aut] (Function interface of matrix operation), Gael Guennebaud [ctb] (Eigenvalue solvers from the 'Eigen' library), Jitse Niesen [ctb] (Eigenvalue solvers from the 'Eigen' library)", + "Maintainer": "Yixuan Qiu ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "Rcpp": { + "Package": "Rcpp", + "Version": "1.1.0", + "Source": "Repository", + "Title": "Seamless R and C++ Integration", + "Date": "2025-07-01", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"JJ\", \"Allaire\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Kevin\", \"Ushey\", role = \"aut\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Qiang\", \"Kou\", role = \"aut\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Nathan\", \"Russell\", role = \"aut\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"John\", \"Chambers\", role = \"aut\"))", + "Description": "The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. 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Also included is a small Windows port of 'mmap' which is released under the MIT license.", + "License": "GPL (>= 2)", + "Depends": [ + "R (>= 3.1)" + ], + "Imports": [ + "methods", + "Rcpp" + ], + "LinkingTo": [ + "Rcpp" + ], + "Suggests": [ + "tinytest" + ], + "URL": "https://github.com/eddelbuettel/rcppannoy, https://dirk.eddelbuettel.com/code/rcpp.annoy.html", + "BugReports": "https://github.com/eddelbuettel/rcppannoy/issues", + "NeedsCompilation": "yes", + "RoxygenNote": "7.1.1", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "RcppArmadillo": { + "Package": "RcppArmadillo", + "Version": "14.6.0-1", + "Source": "Repository", + "Type": "Package", + "Title": "'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library", + "Date": "2025-07-02", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Binxiang\", \"Ni\", role = \"aut\"), person(\"Conrad\", \"Sanderson\", role = \"aut\", comment = c(ORCID = \"0000-0002-0049-4501\")))", + "Description": "'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.", + "License": "GPL (>= 2)", + "LazyLoad": "yes", + "Depends": [ + "R (>= 3.3.0)" + ], + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "Rcpp (>= 1.0.12)", + "stats", + "utils", + "methods" + ], + "Suggests": [ + "tinytest", + "Matrix (>= 1.3.0)", + "pkgKitten", + "reticulate", + "slam" + ], + "URL": "https://github.com/RcppCore/RcppArmadillo, https://dirk.eddelbuettel.com/code/rcpp.armadillo.html", + "BugReports": "https://github.com/RcppCore/RcppArmadillo/issues", + "RoxygenNote": "6.0.1", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Romain Francois [aut] (ORCID: ), Doug Bates [aut] (ORCID: ), Binxiang Ni [aut], Conrad Sanderson [aut] (ORCID: )", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "RcppEigen": { + "Package": "RcppEigen", + "Version": "0.3.4.0.2", + "Source": "Repository", + "Type": "Package", + "Title": "'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library", + "Date": "2024-08-23", + "Authors@R": "c(person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Yixuan\", \"Qiu\", role = \"aut\", comment = c(ORCID = \"0000-0003-0109-6692\")), person(\"Authors of\", \"Eigen\", role = \"cph\", comment = \"Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS\"))", + "Copyright": "See the file COPYRIGHTS for various Eigen copyright details", + "Description": "R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems. Its performance on many algorithms is comparable with some of the best implementations based on 'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header files from the 'Eigen' C++ template library. Thus users do not need to install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2); earlier version were licensed under the GNU LGPL version 3 or later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.", + "License": "GPL (>= 2) | file LICENSE", + "LazyLoad": "yes", + "Depends": [ + "R (>= 3.6.0)" + ], + "LinkingTo": [ + "Rcpp" + ], + "Imports": [ + "Rcpp (>= 0.11.0)", + "stats", + "utils" + ], + "Suggests": [ + "Matrix", + "inline", + "tinytest", + "pkgKitten", + "microbenchmark" + ], + "URL": "https://github.com/RcppCore/RcppEigen, https://dirk.eddelbuettel.com/code/rcpp.eigen.html", + "BugReports": "https://github.com/RcppCore/RcppEigen/issues", + "NeedsCompilation": "yes", + "Author": "Doug Bates [aut] (), Dirk Eddelbuettel [aut, cre] (), Romain Francois [aut] (), Yixuan Qiu [aut] (), Authors of Eigen [cph] (Authorship and copyright in included Eigen library as detailed in inst/COPYRIGHTS)", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "RcppHNSW": { + "Package": "RcppHNSW", + "Version": "0.6.0", + "Source": "Repository", + "Title": "'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors", + "Authors@R": "c( person(\"James\", \"Melville\", , \"jlmelville@gmail.com\", role = c(\"aut\", \"cre\", \"cph\")), person(\"Aaron\", \"Lun\", role = \"ctb\"), person(\"Samuel\", \"Granjeaud\", role = \"ctb\"), person(\"Dmitriy\", \"Selivanov\", role = \"ctb\"), person(\"Yuxing\", \"Liao\", role = \"ctb\") )", + "Description": "'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This package provides a minimal R interface by relying on the 'Rcpp' package. See for more on 'hnswlib'. 'hnswlib' is released under Version 2.0 of the Apache License.", + "License": "GPL (>= 3)", + "URL": "https://github.com/jlmelville/rcpphnsw", + "BugReports": "https://github.com/jlmelville/rcpphnsw/issues", + "Imports": [ + "methods", + "Rcpp (>= 0.11.3)" + ], + "Suggests": [ + "covr", + "testthat" + ], + "LinkingTo": [ + "Rcpp" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "James Melville [aut, cre, cph], Aaron Lun [ctb], Samuel Granjeaud [ctb], Dmitriy Selivanov [ctb], Yuxing Liao [ctb]", + "Maintainer": "James Melville ", + "Repository": "CRAN" + }, + "RcppProgress": { + "Package": "RcppProgress", + "Version": "0.4.2", + "Source": "Repository", + "Maintainer": "Karl Forner ", + "License": "GPL (>= 3)", + "Title": "An Interruptible Progress Bar with OpenMP Support for C++ in R Packages", + "Type": "Package", + "LazyLoad": "yes", + "Author": "Karl Forner ", + "Description": "Allows to display a progress bar in the R console for long running computations taking place in c++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.", + "URL": "https://github.com/kforner/rcpp_progress", + "BugReports": "https://github.com/kforner/rcpp_progress/issues", + "Date": "2020-02-06", + "Suggests": [ + "RcppArmadillo", + "devtools", + "roxygen2", + "testthat" + ], + "RoxygenNote": "6.1.1", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "RcppTOML": { + "Package": "RcppTOML", + "Version": "0.2.3", + "Source": "Repository", + "Type": "Package", + "Title": "'Rcpp' Bindings to Parser for \"Tom's Obvious Markup Language\"", + "Date": "2025-03-08", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Mark\", \"Gillard\", role = \"aut\", comment = \"Author of 'toml++' header library\"))", + "Description": "The configuration format defined by 'TOML' (which expands to \"Tom's Obvious Markup Language\") specifies an excellent format (described at ) suitable for both human editing as well as the common uses of a machine-readable format. This package uses 'Rcpp' to connect to the 'toml++' parser written by Mark Gillard to R.", + "SystemRequirements": "A C++17 compiler", + "BugReports": "https://github.com/eddelbuettel/rcpptoml/issues", + "URL": "http://dirk.eddelbuettel.com/code/rcpp.toml.html", + "Imports": [ + "Rcpp (>= 1.0.8)" + ], + "Depends": [ + "R (>= 3.3.0)" + ], + "LinkingTo": [ + "Rcpp" + ], + "Suggests": [ + "tinytest" + ], + "License": "GPL (>= 2)", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (), Mark Gillard [aut] (Author of 'toml++' header library)", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "Rmagic": { + "Package": "Rmagic", + "Version": "2.0.3.999", + "Source": "unknown", + "Type": "Package", + "Title": "MAGIC - Markov Affinity-Based Graph Imputation of Cells", + "Authors@R": "c(person(given = \"David\", family = \"van Dijk\", role = \"aut\", email = \"davidvandijk@gmail.com\"), person(given = \"Scott\", family = \"Gigante\", role = \"cre\", email = \"scott.gigante@yale.edu\", comment = c(ORCID = \"0000-0002-4544-2764\")))", + "Maintainer": "Scott Gigante ", + "Description": "MAGIC (Markov affinity-based graph imputation of cells) is a method for addressing technical noise in single-cell data, including under-sampling of mRNA molecules, often termed \"dropout\" which can severely obscure important gene-gene relationships. 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(2018) .", + "License": "GPL-2 | file LICENSE", + "Depends": [ + "Matrix (>= 1.2-0)", + "R (>= 3.3)" + ], + "Imports": [ + "ggplot2", + "methods", + "reticulate (>= 1.4)", + "stats" + ], + "Suggests": [ + "phateR", + "readr", + "Seurat (>= 3.0.0)", + "viridis" + ], + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.1.1", + "Author": "David van Dijk [aut], Scott Gigante [cre] (ORCID: )" + }, + "Rtsne": { + "Package": "Rtsne", + "Version": "0.17", + "Source": "Repository", + "Type": "Package", + "Title": "T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation", + "Authors@R": "c( person(\"Jesse\", \"Krijthe\", ,\"jkrijthe@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Laurens\", \"van der Maaten\", role = c(\"cph\"), comment = \"Author of original C++ code\") )", + "Description": "An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation by Van der Maaten (see for more information on the original implementation).", + "License": "file LICENSE", + "URL": "https://github.com/jkrijthe/Rtsne", + "Encoding": "UTF-8", + "Imports": [ + "Rcpp (>= 0.11.0)", + "stats" + ], + "LinkingTo": [ + "Rcpp" + ], + "Suggests": [ + "irlba", + "testthat" + ], + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Jesse Krijthe [aut, cre], Laurens van der Maaten [cph] (Author of original C++ code)", + "Maintainer": "Jesse Krijthe ", + "License_is_FOSS": "yes", + "Repository": "CRAN" + }, + "SAVER": { + "Package": "SAVER", + "Version": "1.1.2", + "Source": "Repository", + "Type": "Package", + "Title": "Single-Cell RNA-Seq Gene Expression Recovery", + "Description": "An implementation of a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data. 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\"shreyas.singh.298@gmail.com\"), person(given = \"Laurens\", family = \"Geffert\", role = \"ctb\", email = \"laurensgeffert@gmail.com\"), person(given = \"Hong\", family = \"Ooi\", role = \"ctb\", email = \"hongooi@microsoft.com\"), person(given = \"Henrik\", family = \"Bengtsson\", role = \"ctb\", email = \"henrikb@braju.com\"), person(given = \"Eduard\", family = \"Szocs\", role = \"ctb\", email = \"eduardszoecs@gmail.com\"), person(given = \"David\", family = \"Hugh-Jones\", role = \"ctb\", email = \"davidhughjones@gmail.com\"), person(given = \"Matthieu\", family = \"Stigler\", role = \"ctb\", email = \"Matthieu.Stigler@gmail.com\"), person(given = \"Hugo\", family = \"Tavares\", role = \"ctb\", email = \"hm533@cam.ac.uk\", comment = c(ORCID = \"0000-0001-9373-2726\")), person(given = \"R. Willem\", family = \"Vervoort\", role = \"ctb\", email = \"Willemvervoort@gmail.com\"), person(given = \"Brenton M.\", family = \"Wiernik\", role = \"ctb\", email = \"brenton@wiernik.org\"), person(given = \"Josh\", family = \"Yamamoto\", role = \"ctb\", email = \"joshuayamamoto5@gmail.com\"), person(given = \"Jasme\", family = \"Lee\", role = \"ctb\"), person(given = \"Taren\", family = \"Sanders\", role = \"ctb\", email = \"taren.sanders@acu.edu.au\", comment = c(ORCID = \"0000-0002-4504-6008\")), person(given = \"Ilaria\", family = \"Prosdocimi\", role = \"ctb\", email = \"prosdocimi.ilaria@gmail.com\", comment = c(ORCID = \"0000-0001-8565-094X\")), person(given = \"Daniel D.\", family = \"Sjoberg\", role = \"ctb\", email = \"danield.sjoberg@gmail.com\", comment = c(ORCID = \"0000-0003-0862-2018\")), person(given = \"Alex\", family = \"Reinhart\", role = \"ctb\", email = \"areinhar@stat.cmu.edu\", comment = c(ORCID = \"0000-0002-6658-514X\")))", + "Description": "Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", + "License": "MIT + file LICENSE", + "URL": "https://broom.tidymodels.org/, https://github.com/tidymodels/broom", + "BugReports": "https://github.com/tidymodels/broom/issues", + "Depends": [ + "R (>= 3.5)" + ], + "Imports": [ + "backports", + "cli", + "dplyr (>= 1.0.0)", + "generics (>= 0.0.2)", + "glue", + "lifecycle", + "purrr", + "rlang (>= 1.1.0)", + "stringr", + "tibble (>= 3.0.0)", + "tidyr (>= 1.0.0)" + ], + "Suggests": [ + "AER", + "AUC", + "bbmle", + "betareg (>= 3.2-1)", + "biglm", + "binGroup", + "boot", + "btergm (>= 1.10.6)", + "car (>= 3.1-2)", + "carData", + "caret", + "cluster", + "cmprsk", + "coda", + "covr", + "drc", + "e1071", + "emmeans", + "epiR", + "ergm (>= 3.10.4)", + "fixest (>= 0.9.0)", + "gam (>= 1.15)", + "gee", + "geepack", + "ggplot2", + "glmnet", + "glmnetUtils", + "gmm", + "Hmisc", + "irlba", + "interp", + "joineRML", + "Kendall", + "knitr", + "ks", + "Lahman", + "lavaan (>= 0.6.18)", + "leaps", + "lfe", + "lm.beta", + "lme4", + "lmodel2", + "lmtest (>= 0.9.38)", + "lsmeans", + "maps", + "margins", + "MASS", + "mclust", + "mediation", + "metafor", + "mfx", + "mgcv", + "mlogit", + "modeldata", + "modeltests (>= 0.1.6)", + "muhaz", + "multcomp", + "network", + "nnet", + "ordinal", + "plm", + "poLCA", + "psych", + "quantreg", + "rmarkdown", + "robust", + "robustbase", + "rsample", + "sandwich", + "spdep (>= 1.1)", + "spatialreg", + "speedglm", + "spelling", + "survey", + "survival (>= 3.6-4)", + "systemfit", + "testthat (>= 3.0.0)", + "tseries", + "vars", + "zoo" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Language": "en-US", + "Collate": "'aaa-documentation-helper.R' 'null-and-default.R' 'aer.R' 'auc.R' 'base.R' 'bbmle.R' 'betareg.R' 'biglm.R' 'bingroup.R' 'boot.R' 'broom-package.R' 'broom.R' 'btergm.R' 'car.R' 'caret.R' 'cluster.R' 'cmprsk.R' 'data-frame.R' 'deprecated-0-7-0.R' 'drc.R' 'emmeans.R' 'epiR.R' 'ergm.R' 'fixest.R' 'gam.R' 'geepack.R' 'glmnet-cv-glmnet.R' 'glmnet-glmnet.R' 'gmm.R' 'hmisc.R' 'import-standalone-obj-type.R' 'import-standalone-types-check.R' 'joinerml.R' 'kendall.R' 'ks.R' 'lavaan.R' 'leaps.R' 'lfe.R' 'list-irlba.R' 'list-optim.R' 'list-svd.R' 'list-xyz.R' 'list.R' 'lm-beta.R' 'lmodel2.R' 'lmtest.R' 'maps.R' 'margins.R' 'mass-fitdistr.R' 'mass-negbin.R' 'mass-polr.R' 'mass-ridgelm.R' 'stats-lm.R' 'mass-rlm.R' 'mclust.R' 'mediation.R' 'metafor.R' 'mfx.R' 'mgcv.R' 'mlogit.R' 'muhaz.R' 'multcomp.R' 'nnet.R' 'nobs.R' 'ordinal-clm.R' 'ordinal-clmm.R' 'plm.R' 'polca.R' 'psych.R' 'stats-nls.R' 'quantreg-nlrq.R' 'quantreg-rq.R' 'quantreg-rqs.R' 'robust-glmrob.R' 'robust-lmrob.R' 'robustbase-glmrob.R' 'robustbase-lmrob.R' 'sp.R' 'spdep.R' 'speedglm-speedglm.R' 'speedglm-speedlm.R' 'stats-anova.R' 'stats-arima.R' 'stats-decompose.R' 'stats-factanal.R' 'stats-glm.R' 'stats-htest.R' 'stats-kmeans.R' 'stats-loess.R' 'stats-mlm.R' 'stats-prcomp.R' 'stats-smooth.spline.R' 'stats-summary-lm.R' 'stats-time-series.R' 'survey.R' 'survival-aareg.R' 'survival-cch.R' 'survival-coxph.R' 'survival-pyears.R' 'survival-survdiff.R' 'survival-survexp.R' 'survival-survfit.R' 'survival-survreg.R' 'systemfit.R' 'tseries.R' 'utilities.R' 'vars.R' 'zoo.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "David Robinson [aut], Alex Hayes [aut] (), Simon Couch [aut, cre] (), Posit Software, PBC [cph, fnd], Indrajeet Patil [ctb] (), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (), Jasper Cooper [ctb] (), E Auden Krauska [ctb] (), Alex Wang [ctb], Malcolm Barrett [ctb] (), Charles Gray [ctb] (), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (), Eduard Szoecs [ctb], Frederik Aust [ctb] (), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (), Bruna Wundervald [ctb] (), Joyce Cahoon [ctb] (), Grant McDermott [ctb] (), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (), Lukas Wallrich [ctb] (), James Martherus [ctb] (), Chuliang Xiao [ctb] (), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (), Ilaria Prosdocimi [ctb] (), Daniel D. Sjoberg [ctb] (), Alex Reinhart [ctb] ()", + "Maintainer": "Simon Couch ", + "Repository": "CRAN" + }, + "bslib": { + "Package": "bslib", + "Version": "0.9.0", + "Source": "Repository", + "Title": "Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'", + "Authors@R": "c( person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Garrick\", \"Aden-Buie\", , \"garrick@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-7111-0077\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Javi\", \"Aguilar\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap colorpicker library\"), person(\"Thomas\", \"Park\", role = c(\"ctb\", \"cph\"), comment = \"Bootswatch library\"), person(, \"PayPal\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap accessibility plugin\") )", + "Description": "Simplifies custom 'CSS' styling of both 'shiny' and 'rmarkdown' via 'Bootstrap' 'Sass'. Supports 'Bootstrap' 3, 4 and 5 as well as their various 'Bootswatch' themes. 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This packages does exactly that.", + "License": "MIT + file LICENSE", + "URL": "https://callr.r-lib.org, https://github.com/r-lib/callr", + "BugReports": "https://github.com/r-lib/callr/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "processx (>= 3.6.1)", + "R6", + "utils" + ], + "Suggests": [ + "asciicast (>= 2.3.1)", + "cli (>= 1.1.0)", + "mockery", + "ps", + "rprojroot", + "spelling", + "testthat (>= 3.2.0)", + "withr (>= 2.3.0)" + ], + "Config/Needs/website": "r-lib/asciicast, glue, htmlwidgets, igraph, tibble, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.1.9000", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre, cph] (), Winston Chang [aut], Posit Software, PBC [cph, fnd], Ascent Digital Services [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository", + "Title": "Translate Spreadsheet Cell Ranges to Rows and Columns", + "Authors@R": "c( person(\"Jennifer\", \"Bryan\", , \"jenny@stat.ubc.ca\", c(\"cre\", \"aut\")), person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", \"ctb\") )", + "Description": "Helper functions to work with spreadsheets and the \"A1:D10\" style of cell range specification.", + "Depends": [ + "R (>= 3.0.0)" + ], + "License": "MIT + file LICENSE", + "LazyData": "true", + "URL": "https://github.com/rsheets/cellranger", + "BugReports": "https://github.com/rsheets/cellranger/issues", + "Suggests": [ + "covr", + "testthat (>= 1.0.0)", + "knitr", + "rmarkdown" + ], + "RoxygenNote": "5.0.1.9000", + "VignetteBuilder": "knitr", + "Imports": [ + "rematch", + "tibble" + ], + "NeedsCompilation": "no", + "Author": "Jennifer Bryan [cre, aut], Hadley Wickham [ctb]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "cli": { + "Package": "cli", + "Version": "3.6.5", + "Source": "Repository", + "Title": "Helpers for Developing Command Line Interfaces", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"gabor@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Kirill\", \"Müller\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", , \"salim-b@pm.me\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.", + "License": "MIT + file LICENSE", + "URL": "https://cli.r-lib.org, https://github.com/r-lib/cli", + "BugReports": "https://github.com/r-lib/cli/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "utils" + ], + "Suggests": [ + "callr", + "covr", + "crayon", + "digest", + "glue (>= 1.6.0)", + "grDevices", + "htmltools", + "htmlwidgets", + "knitr", + "methods", + "processx", + "ps (>= 1.3.4.9000)", + "rlang (>= 1.0.2.9003)", + "rmarkdown", + "rprojroot", + "rstudioapi", + "testthat (>= 3.2.0)", + "tibble", + "whoami", + "withr" + ], + "Config/Needs/website": "r-lib/asciicast, bench, brio, cpp11, decor, desc, fansi, prettyunits, sessioninfo, tidyverse/tidytemplate, usethis, vctrs", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Hadley Wickham [ctb], Kirill Müller [ctb], Salim Brüggemann [ctb] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "clipr": { + "Package": "clipr", + "Version": "0.8.0", + "Source": "Repository", + "Type": "Package", + "Title": "Read and Write from the System Clipboard", + "Authors@R": "c( person(\"Matthew\", \"Lincoln\", , \"matthew.d.lincoln@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4387-3384\")), person(\"Louis\", \"Maddox\", role = \"ctb\"), person(\"Steve\", \"Simpson\", role = \"ctb\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\") )", + "Description": "Simple utility functions to read from and write to the Windows, OS X, and X11 clipboards.", + "License": "GPL-3", + "URL": "https://github.com/mdlincoln/clipr, http://matthewlincoln.net/clipr/", + "BugReports": "https://github.com/mdlincoln/clipr/issues", + "Imports": [ + "utils" + ], + "Suggests": [ + "covr", + "knitr", + "rmarkdown", + "rstudioapi (>= 0.5)", + "testthat (>= 2.0.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.1.2", + "SystemRequirements": "xclip (https://github.com/astrand/xclip) or xsel (http://www.vergenet.net/~conrad/software/xsel/) for accessing the X11 clipboard, or wl-clipboard (https://github.com/bugaevc/wl-clipboard) for systems using Wayland.", + "NeedsCompilation": "no", + "Author": "Matthew Lincoln [aut, cre] (), Louis Maddox [ctb], Steve Simpson [ctb], Jennifer Bryan [ctb]", + "Maintainer": "Matthew Lincoln ", + "Repository": "CRAN" + }, + "cluster": { + "Package": "cluster", + "Version": "2.1.8.1", + "Source": "Repository", + "VersionNote": "Last CRAN: 2.1.8 on 2024-12-10; 2.1.7 on 2024-12-06; 2.1.6 on 2023-11-30; 2.1.5 on 2023-11-27", + "Date": "2025-03-11", + "Priority": "recommended", + "Title": "\"Finding Groups in Data\": Cluster Analysis Extended Rousseeuw et al.", + "Description": "Methods for Cluster analysis. 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This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. 'conflicted' takes a different approach, making every conflict an error and forcing you to choose which function to use.", + "License": "MIT + file LICENSE", + "URL": "https://conflicted.r-lib.org/, https://github.com/r-lib/conflicted", + "BugReports": "https://github.com/r-lib/conflicted/issues", + "Depends": [ + "R (>= 3.2)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "memoise", + "rlang (>= 1.0.0)" + ], + "Suggests": [ + "callr", + "covr", + "dplyr", + "Matrix", + "methods", + "pkgload", + "testthat (>= 3.0.0)", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], RStudio [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "cowplot": { + "Package": "cowplot", + "Version": "1.1.3", + "Source": "Repository", + "Title": "Streamlined Plot Theme and Plot Annotations for 'ggplot2'", + "Authors@R": "person( given = \"Claus O.\", family = \"Wilke\", role = c(\"aut\", \"cre\"), email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\") )", + "Description": "Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.", + "URL": "https://wilkelab.org/cowplot/", + "BugReports": "https://github.com/wilkelab/cowplot/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "ggplot2 (>= 3.4.0)", + "grid", + "gtable", + "grDevices", + "methods", + "rlang", + "scales" + ], + "License": "GPL-2", + "Suggests": [ + "Cairo", + "covr", + "dplyr", + "forcats", + "gridGraphics (>= 0.4-0)", + "knitr", + "lattice", + "magick", + "maps", + "PASWR", + "patchwork", + "rmarkdown", + "ragg", + "testthat (>= 1.0.0)", + "tidyr", + "vdiffr (>= 0.3.0)", + "VennDiagram" + ], + "VignetteBuilder": "knitr", + "Collate": "'add_sub.R' 'align_plots.R' 'as_grob.R' 'as_gtable.R' 'axis_canvas.R' 'cowplot.R' 'draw.R' 'get_plot_component.R' 'get_axes.R' 'get_titles.R' 'get_legend.R' 'get_panel.R' 'gtable.R' 'key_glyph.R' 'plot_grid.R' 'save.R' 'set_null_device.R' 'setup.R' 'stamp.R' 'themes.R' 'utils_ggplot2.R'", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Claus O. 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Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (), Jim Hester [aut] (), Romain François [aut] (), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.3", + "Source": "Repository", + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ + "grDevices", + "methods", + "utils" + ], + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "credentials": { + "Package": "credentials", + "Version": "2.0.2", + "Source": "Repository", + "Type": "Package", + "Title": "Tools for Managing SSH and Git Credentials", + "Authors@R": "person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\"))", + "Description": "Setup and retrieve HTTPS and SSH credentials for use with 'git' and other services. For HTTPS remotes the package interfaces the 'git-credential' utility which 'git' uses to store HTTP usernames and passwords. For SSH remotes we provide convenient functions to find or generate appropriate SSH keys. The package both helps the user to setup a local git installation, and also provides a back-end for git/ssh client libraries to authenticate with existing user credentials.", + "License": "MIT + file LICENSE", + "SystemRequirements": "git (optional)", + "Encoding": "UTF-8", + "Imports": [ + "openssl (>= 1.3)", + "sys (>= 2.1)", + "curl", + "jsonlite", + "askpass" + ], + "Suggests": [ + "testthat", + "knitr", + "rmarkdown" + ], + "RoxygenNote": "7.2.1", + "VignetteBuilder": "knitr", + "Language": "en-US", + "URL": "https://docs.ropensci.org/credentials/ https://r-lib.r-universe.dev/credentials", + "BugReports": "https://github.com/r-lib/credentials/issues", + "NeedsCompilation": "no", + "Author": "Jeroen Ooms [aut, cre] ()", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "crosstalk": { + "Package": "crosstalk", + "Version": "1.2.1", + "Source": "Repository", + "Type": "Package", + "Title": "Inter-Widget Interactivity for HTML Widgets", + "Authors@R": "c( person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@posit.co\"), person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@posit.co\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(family = \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", + "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). 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Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.73): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" + ], + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2.9000", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" + }, + "data.table": { + "Package": "data.table", + "Version": "1.17.8", + "Source": "Repository", + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", + "License": "MPL-2.0 | file LICENSE", + "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", + "BugReports": "https://github.com/Rdatatable/data.table/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "ByteCompile": "TRUE", + "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\"), person(\"Michael\",\"Chirico\", role=\"aut\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", comment = c(ORCID=\"0000-0002-3146-0865\")), person(\"Benjamin\",\"Schwendinger\",role=\"aut\", comment = c(ORCID=\"0000-0003-3315-8114\")), person(\"Ivan\", 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[aut] (ORCID: ), Toby Hocking [aut] (ORCID: ), Benjamin Schwendinger [aut] (ORCID: ), Ivan Krylov [aut] (ORCID: ), Pasha Stetsenko [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb], Markus Bonsch [ctb], Hugh Parsonage [ctb], Scott Ritchie [ctb], Kun Ren [ctb], Xianying Tan [ctb], Rick Saporta [ctb], Otto Seiskari [ctb], Xianghui Dong [ctb], Michel Lang [ctb], Watal Iwasaki [ctb], Seth Wenchel [ctb], Karl Broman [ctb], Tobias Schmidt [ctb], David Arenburg [ctb], Ethan Smith [ctb], Francois Cocquemas [ctb], Matthieu Gomez [ctb], Philippe Chataignon [ctb], Nello Blaser [ctb], Dmitry Selivanov [ctb], Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb], @marc-outins [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan 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"Source": "Repository", + "Type": "Package", + "Title": "A 'dplyr' Back End for Databases", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Maximilian\", \"Girlich\", role = \"aut\"), person(\"Edgar\", \"Ruiz\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.", + "License": "MIT + file LICENSE", + "URL": "https://dbplyr.tidyverse.org/, https://github.com/tidyverse/dbplyr", + "BugReports": "https://github.com/tidyverse/dbplyr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "blob (>= 1.2.0)", + "cli (>= 3.6.1)", + "DBI (>= 1.1.3)", + "dplyr (>= 1.1.2)", + "glue (>= 1.6.2)", + "lifecycle (>= 1.0.3)", + "magrittr", + "methods", + "pillar (>= 1.9.0)", + "purrr (>= 1.0.1)", + "R6 (>= 2.2.2)", + "rlang (>= 1.1.1)", + "tibble (>= 3.2.1)", + "tidyr (>= 1.3.0)", + "tidyselect (>= 1.2.1)", + "utils", + "vctrs (>= 0.6.3)", + "withr (>= 2.5.0)" + ], + "Suggests": [ + "bit64", + "covr", + "knitr", + "Lahman", + "nycflights13", + "odbc (>= 1.4.2)", + "RMariaDB (>= 1.2.2)", + "rmarkdown", + "RPostgres (>= 1.4.5)", + "RPostgreSQL", + "RSQLite (>= 2.3.1)", + "testthat (>= 3.1.10)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", + "Encoding": "UTF-8", + "Language": "en-gb", + "RoxygenNote": "7.3.1", + "Collate": "'db-sql.R' 'utils-check.R' 'import-standalone-types-check.R' 'import-standalone-obj-type.R' 'utils.R' 'sql.R' 'escape.R' 'translate-sql-cut.R' 'translate-sql-quantile.R' 'translate-sql-string.R' 'translate-sql-paste.R' 'translate-sql-helpers.R' 'translate-sql-window.R' 'translate-sql-conditional.R' 'backend-.R' 'backend-access.R' 'backend-hana.R' 'backend-hive.R' 'backend-impala.R' 'verb-copy-to.R' 'backend-mssql.R' 'backend-mysql.R' 'backend-odbc.R' 'backend-oracle.R' 'backend-postgres.R' 'backend-postgres-old.R' 'backend-redshift.R' 'backend-snowflake.R' 'backend-spark-sql.R' 'backend-sqlite.R' 'backend-teradata.R' 'build-sql.R' 'data-cache.R' 'data-lahman.R' 'data-nycflights13.R' 'db-escape.R' 'db-io.R' 'db.R' 'dbplyr.R' 'explain.R' 'ident.R' 'import-standalone-s3-register.R' 'join-by-compat.R' 'join-cols-compat.R' 'lazy-join-query.R' 'lazy-ops.R' 'lazy-query.R' 'lazy-select-query.R' 'lazy-set-op-query.R' 'memdb.R' 'optimise-utils.R' 'pillar.R' 'progress.R' 'sql-build.R' 'query-join.R' 'query-select.R' 'query-semi-join.R' 'query-set-op.R' 'query.R' 'reexport.R' 'remote.R' 'rows.R' 'schema.R' 'simulate.R' 'sql-clause.R' 'sql-expr.R' 'src-sql.R' 'src_dbi.R' 'table-name.R' 'tbl-lazy.R' 'tbl-sql.R' 'test-frame.R' 'testthat.R' 'tidyeval-across.R' 'tidyeval.R' 'translate-sql.R' 'utils-format.R' 'verb-arrange.R' 'verb-compute.R' 'verb-count.R' 'verb-distinct.R' 'verb-do-query.R' 'verb-do.R' 'verb-expand.R' 'verb-fill.R' 'verb-filter.R' 'verb-group_by.R' 'verb-head.R' 'verb-joins.R' 'verb-mutate.R' 'verb-pivot-longer.R' 'verb-pivot-wider.R' 'verb-pull.R' 'verb-select.R' 'verb-set-ops.R' 'verb-slice.R' 'verb-summarise.R' 'verb-uncount.R' 'verb-window.R' 'zzz.R'", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Maximilian Girlich [aut], Edgar Ruiz [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "deldir": { + "Package": "deldir", + "Version": "2.0-4", + "Source": "Repository", + "Date": "2024-02-27", + "Title": "Delaunay Triangulation and Dirichlet (Voronoi) Tessellation", + "Author": "Rolf Turner", + "Maintainer": "Rolf Turner ", + "Depends": [ + "R (>= 3.5.0)" + ], + "Suggests": [ + "polyclip" + ], + "Imports": [ + "graphics", + "grDevices" + ], + "Description": "Calculates the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. Plots triangulations and tessellations in various ways. Clips tessellations to sub-windows. Calculates perimeters of tessellations. Summarises information about the tiles of the tessellation.\tCalculates the centroidal Voronoi (Dirichlet) tessellation using Lloyd's algorithm.", + "LazyData": "true", + "ByteCompile": "true", + "License": "GPL (>= 2)", + "NeedsCompilation": "yes", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "desc": { + "Package": "desc", + "Version": "1.4.3", + "Source": "Repository", + "Title": "Manipulate DESCRIPTION Files", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", role = \"aut\"), person(\"Jim\", \"Hester\", , \"james.f.hester@gmail.com\", role = \"aut\"), person(\"Maëlle\", \"Salmon\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2815-0399\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Maintainer": "Gábor Csárdi ", + "Description": "Tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.", + "License": "MIT + file LICENSE", + "URL": "https://desc.r-lib.org/, https://github.com/r-lib/desc", + "BugReports": "https://github.com/r-lib/desc/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "cli", + "R6", + "utils" + ], + "Suggests": [ + "callr", + "covr", + "gh", + "spelling", + "testthat", + "whoami", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3", + "Collate": "'assertions.R' 'authors-at-r.R' 'built.R' 'classes.R' 'collate.R' 'constants.R' 'deps.R' 'desc-package.R' 'description.R' 'encoding.R' 'find-package-root.R' 'latex.R' 'non-oo-api.R' 'package-archives.R' 'read.R' 'remotes.R' 'str.R' 'syntax_checks.R' 'urls.R' 'utils.R' 'validate.R' 'version.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Kirill Müller [aut], Jim Hester [aut], Maëlle Salmon [ctb] (), Posit Software, PBC [cph, fnd]", + "Repository": "CRAN" + }, + "digest": { + "Package": "digest", + "Version": "0.6.37", + "Source": "Repository", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\"), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\"), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\"), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\"), person(\"Ion\", \"Suruceanu\", role=\"ctb\"), person(\"Bill\", \"Denney\", role=\"ctb\"), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\"), person(\"Sergey\", \"Fedorov\", role=\"ctb\"), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\"), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\"))", + "Date": "2024-08-19", + "Title": "Create Compact Hash Digests of R Objects", + "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "utils" + ], + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (), Antoine Lucas [ctb], Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (), Simon Urbanek [ctb] (), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb], Duncan Murdoch [ctb], Jim Hester [ctb], Wush Wu [ctb] (), Qiang Kou [ctb] (), Thierry Onkelinx [ctb] (), Michel Lang [ctb] (), Viliam Simko [ctb], Kurt Hornik [ctb] (), Radford Neal [ctb] (), Kendon Bell [ctb] (), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb], Ion Suruceanu [ctb], Bill Denney [ctb], Dirk Schumacher [ctb], András Svraka [ctb], Sergey Fedorov [ctb], Will Landau [ctb] (), Floris Vanderhaeghe [ctb] (), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (), Mark van der Loo [ctb] (), Chris Muir [ctb] (), Moritz Beller [ctb] (), Sebastian Campbell [ctb], Winston Chang [ctb] (), Dean Attali [ctb] (), Michael Chirico [ctb] (), Kevin Ushey [ctb]", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" + }, + "doParallel": { + "Package": "doParallel", + "Version": "1.0.17", + "Source": "Repository", + "Type": "Package", + "Title": "Foreach Parallel Adaptor for the 'parallel' Package", + "Authors@R": "c(person(\"Folashade\", \"Daniel\", role=\"cre\", email=\"fdaniel@microsoft.com\"), person(\"Microsoft\", \"Corporation\", role=c(\"aut\", \"cph\")), person(\"Steve\", \"Weston\", role=\"aut\"), person(\"Dan\", \"Tenenbaum\", role=\"ctb\"))", + "Description": "Provides a parallel backend for the %dopar% function using the parallel package.", + "Depends": [ + "R (>= 2.14.0)", + "foreach (>= 1.2.0)", + "iterators (>= 1.0.0)", + "parallel", + "utils" + ], + "Suggests": [ + "caret", + "mlbench", + "rpart", + "RUnit" + ], + "Enhances": [ + "compiler" + ], + "License": "GPL-2", + "URL": "https://github.com/RevolutionAnalytics/doparallel", + "BugReports": "https://github.com/RevolutionAnalytics/doparallel/issues", + "NeedsCompilation": "no", + "Author": "Folashade Daniel [cre], Microsoft Corporation [aut, cph], Steve Weston [aut], Dan Tenenbaum [ctb]", + "Maintainer": "Folashade Daniel ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "dotCall64": { + "Package": "dotCall64", + "Version": "1.2", + "Source": "Repository", + "Type": "Package", + "Title": "Enhanced Foreign Function Interface Supporting Long Vectors", + "Date": "2024-10-03", + "Authors@R": "c(person(\"Kaspar\", \"Moesinger\", role = c(\"aut\"), email = \"kaspar.moesinger@gmail.com\"), person(\"Florian\", \"Gerber\", role = c(\"aut\"), email = \"flora.fauna.gerber@gmail.com\", comment = c(ORCID = \"0000-0001-8545-5263\")), person(\"Reinhard\", \"Furrer\", role = c(\"cre\", \"ctb\"), email = \"reinhard.furrer@uzh.ch\", comment = c(ORCID = \"0000-0002-6319-2332\")))", + "Description": "Provides .C64(), which is an enhanced version of .C() and .Fortran() from the foreign function interface. .C64() supports long vectors, arguments of type 64-bit integer, and provides a mechanism to avoid unnecessary copies of read-only and write-only arguments. This makes it a convenient and fast interface to C/C++ and Fortran code.", + "License": "GPL (>= 2)", + "URL": "https://git.math.uzh.ch/reinhard.furrer/dotCall64", + "BugReports": "https://git.math.uzh.ch/reinhard.furrer/dotCall64/-/issues", + "Depends": [ + "R (>= 4.0)" + ], + "Suggests": [ + "microbenchmark", + "RhpcBLASctl", + "RColorBrewer", + "roxygen2", + "spam", + "testthat" + ], + "Collate": "'vector_dc.R' 'dotCall64.R' 'zzz.R'", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Kaspar Moesinger [aut], Florian Gerber [aut] (), Reinhard Furrer [cre, ctb] ()", + "Maintainer": "Reinhard Furrer ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "dplyr": { + "Package": "dplyr", + "Version": "1.1.4", + "Source": "Repository", + "Type": "Package", + "Title": "A Grammar of Data Manipulation", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Lionel\", \"Henry\", role = \"aut\"), person(\"Kirill\", \"Müller\", role = \"aut\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A fast, consistent tool for working with data frame like objects, both in memory and out of memory.", + "License": "MIT + file LICENSE", + "URL": "https://dplyr.tidyverse.org, https://github.com/tidyverse/dplyr", + "BugReports": "https://github.com/tidyverse/dplyr/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "generics", + "glue (>= 1.3.2)", + "lifecycle (>= 1.0.3)", + "magrittr (>= 1.5)", + "methods", + "pillar (>= 1.9.0)", + "R6", + "rlang (>= 1.1.0)", + "tibble (>= 3.2.0)", + "tidyselect (>= 1.2.0)", + "utils", + "vctrs (>= 0.6.4)" + ], + "Suggests": [ + "bench", + "broom", + "callr", + "covr", + "DBI", + "dbplyr (>= 2.2.1)", + "ggplot2", + "knitr", + "Lahman", + "lobstr", + "microbenchmark", + "nycflights13", + "purrr", + "rmarkdown", + "RMySQL", + "RPostgreSQL", + "RSQLite", + "stringi (>= 1.7.6)", + "testthat (>= 3.1.5)", + "tidyr (>= 1.3.0)", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse, shiny, pkgdown, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre] (), Romain François [aut] (), Lionel Henry [aut], Kirill Müller [aut] (), Davis Vaughan [aut] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "dqrng": { + "Package": "dqrng", + "Version": "0.4.1", + "Source": "Repository", + "Type": "Package", + "Title": "Fast Pseudo Random Number Generators", + "Authors@R": "c( person(\"Ralf\", \"Stubner\", email = \"ralf.stubner@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0009-1908-106X\")), person(\"daqana GmbH\", role = \"cph\"), person(\"David Blackman\", role = \"cph\", comment = \"Xoroshiro / Xoshiro family\"), person(\"Melissa O'Neill\", email = \"oneill@pcg-random.org\", role = \"cph\", comment = \"PCG family\"), person(\"Sebastiano Vigna\", email = \"vigna@acm.org\", role = \"cph\", comment = \"Xoroshiro / Xoshiro family\"), person(\"Aaron\", \"Lun\", role=\"ctb\"), person(\"Kyle\", \"Butts\", role = \"ctb\", email = \"kyle.butts@colorado.edu\"), person(\"Henrik\", \"Sloot\", role = \"ctb\"), person(\"Philippe\", \"Grosjean\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0002-2694-9471\")) )", + "Description": "Several fast random number generators are provided as C++ header only libraries: The PCG family by O'Neill (2014 ) as well as the Xoroshiro / Xoshiro family by Blackman and Vigna (2021 ). In addition fast functions for generating random numbers according to a uniform, normal and exponential distribution are included. The latter two use the Ziggurat algorithm originally proposed by Marsaglia and Tsang (2000, ). The fast sampling methods support unweighted sampling both with and without replacement. These functions are exported to R and as a C++ interface and are enabled for use with the default 64 bit generator from the PCG family, Xoroshiro128+/++/** and Xoshiro256+/++/** as well as the 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011, ) as provided by the package 'sitmo'.", + "License": "AGPL-3", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "Rcpp (>= 0.12.16)" + ], + "LinkingTo": [ + "Rcpp", + "BH (>= 1.64.0-1)", + "sitmo (>= 2.0.0)" + ], + "RoxygenNote": "7.3.1", + "Suggests": [ + "BH", + "testthat", + "knitr", + "rmarkdown", + "mvtnorm (>= 1.2-3)", + "bench", + "sitmo" + ], + "VignetteBuilder": "knitr", + "URL": "https://daqana.github.io/dqrng/, https://github.com/daqana/dqrng", + "BugReports": "https://github.com/daqana/dqrng/issues", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Ralf Stubner [aut, cre] (), daqana GmbH [cph], David Blackman [cph] (Xoroshiro / Xoshiro family), Melissa O'Neill [cph] (PCG family), Sebastiano Vigna [cph] (Xoroshiro / Xoshiro family), Aaron Lun [ctb], Kyle Butts [ctb], Henrik Sloot [ctb], Philippe Grosjean [ctb] ()", + "Maintainer": "Ralf Stubner ", + "Repository": "CRAN" + }, + "dtplyr": { + "Package": "dtplyr", + "Version": "1.3.1", + "Source": "Repository", + "Title": "Data Table Back-End for 'dplyr'", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"cre\", \"aut\")), person(\"Maximilian\", \"Girlich\", role = \"aut\"), person(\"Mark\", \"Fairbanks\", role = \"aut\"), person(\"Ryan\", \"Dickerson\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a data.table backend for 'dplyr'. The goal of 'dtplyr' is to allow you to write 'dplyr' code that is automatically translated to the equivalent, but usually much faster, data.table code.", + "License": "MIT + file LICENSE", + "URL": "https://dtplyr.tidyverse.org, https://github.com/tidyverse/dtplyr", + "BugReports": "https://github.com/tidyverse/dtplyr/issues", + "Depends": [ + "R (>= 3.3)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "data.table (>= 1.13.0)", + "dplyr (>= 1.1.0)", + "glue", + "lifecycle", + "rlang (>= 1.0.4)", + "tibble", + "tidyselect (>= 1.2.0)", + "vctrs (>= 0.4.1)" + ], + "Suggests": [ + "bench", + "covr", + "knitr", + "rmarkdown", + "testthat (>= 3.1.2)", + "tidyr (>= 1.1.0)", + "waldo (>= 0.3.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [cre, aut], Maximilian Girlich [aut], Mark Fairbanks [aut], Ryan Dickerson [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "evaluate": { + "Package": "evaluate", + "Version": "1.0.3", + "Source": "Repository", + "Type": "Package", + "Title": "Parsing and Evaluation Tools that Provide More Details than the Default", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Yihui\", \"Xie\", role = \"aut\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Michael\", \"Lawrence\", role = \"ctb\"), person(\"Thomas\", \"Kluyver\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\"), person(\"Barret\", \"Schloerke\", role = \"ctb\"), person(\"Adam\", \"Ryczkowski\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Michel\", \"Lang\", role = \"ctb\"), person(\"Karolis\", \"Koncevičius\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.", + "License": "MIT + file LICENSE", + "URL": "https://evaluate.r-lib.org/, https://github.com/r-lib/evaluate", + "BugReports": "https://github.com/r-lib/evaluate/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Suggests": [ + "callr", + "covr", + "ggplot2 (>= 3.3.6)", + "lattice", + "methods", + "pkgload", + "rlang", + "knitr", + "testthat (>= 3.0.0)", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Yihui Xie [aut] (), Michael Lawrence [ctb], Thomas Kluyver [ctb], Jeroen Ooms [ctb], Barret Schloerke [ctb], Adam Ryczkowski [ctb], Hiroaki Yutani [ctb], Michel Lang [ctb], Karolis Koncevičius [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "farver": { + "Package": "farver", + "Version": "2.1.2", + "Source": "Repository", + "Type": "Package", + "Title": "High Performance Colour Space Manipulation", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Berendea\", \"Nicolae\", role = \"aut\", comment = \"Author of the ColorSpace C++ library\"), person(\"Romain\", \"François\", , \"romain@purrple.cat\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The encoding of colour can be handled in many different ways, using different colour spaces. As different colour spaces have different uses, efficient conversion between these representations are important. The 'farver' package provides a set of functions that gives access to very fast colour space conversion and comparisons implemented in C++, and offers speed improvements over the 'convertColor' function in the 'grDevices' package.", + "License": "MIT + file LICENSE", + "URL": "https://farver.data-imaginist.com, https://github.com/thomasp85/farver", + "BugReports": "https://github.com/thomasp85/farver/issues", + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (), Berendea Nicolae [aut] (Author of the ColorSpace C++ library), Romain François [aut] (), Posit, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, + "fastDummies": { + "Package": "fastDummies", + "Version": "1.7.5", + "Source": "Repository", + "Type": "Package", + "Title": "Fast Creation of Dummy (Binary) Columns and Rows from Categorical Variables", + "Authors@R": "c( person(\"Jacob\", \"Kaplan\", email = \"jkkaplan6@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0601-0387\")), person(\"Benjamin\", \"Schlegel\", email = \"kontakt@benjaminschlegl.ch\", role = \"ctb\"))", + "Description": "Creates dummy columns from columns that have categorical variables (character or factor types). You can also specify which columns to make dummies out of, or which columns to ignore. Also creates dummy rows from character, factor, and Date columns. 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This package can read and write both the metadata and the cell data in a Sheet.", + "License": "MIT + file LICENSE", + "URL": "https://googlesheets4.tidyverse.org, https://github.com/tidyverse/googlesheets4", + "BugReports": "https://github.com/tidyverse/googlesheets4/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cellranger", + "cli (>= 3.0.0)", + "curl", + "gargle (>= 1.5.0)", + "glue (>= 1.3.0)", + "googledrive (>= 2.1.0)", + "httr", + "ids", + "lifecycle", + "magrittr", + "methods", + "purrr", + "rematch2", + "rlang (>= 1.0.2)", + "tibble (>= 2.1.1)", + "utils", + "vctrs (>= 0.2.3)", + "withr" + ], + "Suggests": [ + "readr", + "rmarkdown", + "spelling", + "testthat (>= 3.1.7)" + ], + "ByteCompile": "true", + "Config/Needs/website": "tidyverse, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Jennifer Bryan [cre, aut] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "gplots": { + "Package": "gplots", + "Version": "3.2.0", + "Source": "Repository", + "Title": "Various R Programming Tools for Plotting Data", + "Description": "Various R programming tools for plotting data, including: - calculating and plotting locally smoothed summary function as ('bandplot', 'wapply'), - enhanced versions of standard plots ('barplot2', 'boxplot2', 'heatmap.2', 'smartlegend'), - manipulating colors ('col2hex', 'colorpanel', 'redgreen', 'greenred', 'bluered', 'redblue', 'rich.colors'), - calculating and plotting two-dimensional data summaries ('ci2d', 'hist2d'), - enhanced regression diagnostic plots ('lmplot2', 'residplot'), - formula-enabled interface to 'stats::lowess' function ('lowess'), - displaying textual data in plots ('textplot', 'sinkplot'), - plotting dots whose size reflects the relative magnitude of the elements ('balloonplot', 'bubbleplot'), - plotting \"Venn\" diagrams ('venn'), - displaying Open-Office style plots ('ooplot'), - plotting multiple data on same region, with separate axes ('overplot'), - plotting means and confidence intervals ('plotCI', 'plotmeans'), - spacing points in an x-y plot so they don't overlap ('space').", + "Depends": [ + "R (>= 3.0)" + ], + "Imports": [ + "gtools", + "stats", + "caTools", + "KernSmooth", + "methods" + ], + "Suggests": [ + "grid", + "MASS", + "knitr", + "rmarkdown", + "r2d2", + "nlme" + ], + "LazyData": "yes", + "VignetteBuilder": "knitr", + "Date": "2024-10-05", + "Authors@R": "c( person(\"Gregory R.\", \"Warnes\", , role = \"aut\"), person(\"Ben\", \"Bolker\", , role = \"aut\"), person(\"Lodewijk\", \"Bonebakker\", , role = \"aut\"), person(\"Robert\", \"Gentleman\", role = \"aut\"), person(\"Wolfgang\", \"Huber\", role = \"aut\"), person(\"Andy\", \"Liaw\", role = \"aut\"), person(\"Thomas\", \"Lumley\", role = \"aut\"), person(\"Martin\", \"Maechler\", role = \"aut\"), person(\"Arni\", \"Magnusson\", role = \"aut\"), person(\"Steffen\", \"Moeller\", role = \"aut\"), person(\"Marc\", \"Schwartz\", role = \"aut\"), person(\"Bill\", \"Venables\", role = \"aut\"), person(\"Tal\", \"Galili\", , \"tal.galili@gmail.com\", c(\"aut\", \"cre\")) )", + "License": "GPL-2", + "URL": "https://github.com/talgalili/gplots, https://talgalili.github.io/gplots/", + "BugReports": "https://github.com/talgalili/gplots/issues", + "NeedsCompilation": "no", + "Author": "Gregory R. Warnes [aut], Ben Bolker [aut], Lodewijk Bonebakker [aut], Robert Gentleman [aut], Wolfgang Huber [aut], Andy Liaw [aut], Thomas Lumley [aut], Martin Maechler [aut], Arni Magnusson [aut], Steffen Moeller [aut], Marc Schwartz [aut], Bill Venables [aut], Tal Galili [aut, cre]", + "Maintainer": "Tal Galili ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "gridExtra": { + "Package": "gridExtra", + "Version": "2.3", + "Source": "Repository", + "Authors@R": "c(person(\"Baptiste\", \"Auguie\", email = \"baptiste.auguie@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Anton\", \"Antonov\", email = \"tonytonov@gmail.com\", role = c(\"ctb\")))", + "License": "GPL (>= 2)", + "Title": "Miscellaneous Functions for \"Grid\" Graphics", + "Type": "Package", + "Description": "Provides a number of user-level functions to work with \"grid\" graphics, notably to arrange multiple grid-based plots on a page, and draw tables.", + "VignetteBuilder": "knitr", + "Imports": [ + "gtable", + "grid", + "grDevices", + "graphics", + "utils" + ], + "Suggests": [ + "ggplot2", + "egg", + "lattice", + "knitr", + "testthat" + ], + "RoxygenNote": "6.0.1", + "NeedsCompilation": "no", + "Author": "Baptiste Auguie [aut, cre], Anton Antonov [ctb]", + "Maintainer": "Baptiste Auguie ", + "Repository": "CRAN" + }, + "gtable": { + "Package": "gtable", + "Version": "0.3.6", + "Source": "Repository", + "Title": "Arrange 'Grobs' in Tables", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Tools to make it easier to work with \"tables\" of 'grobs'. The 'gtable' package defines a 'gtable' grob class that specifies a grid along with a list of grobs and their placement in the grid. Further the package makes it easy to manipulate and combine 'gtable' objects so that complex compositions can be built up sequentially.", + "License": "MIT + file LICENSE", + "URL": "https://gtable.r-lib.org, https://github.com/r-lib/gtable", + "BugReports": "https://github.com/r-lib/gtable/issues", + "Depends": [ + "R (>= 4.0)" + ], + "Imports": [ + "cli", + "glue", + "grid", + "lifecycle", + "rlang (>= 1.1.0)", + "stats" + ], + "Suggests": [ + "covr", + "ggplot2", + "knitr", + "profvis", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2024-10-25", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "CRAN" + }, + "gtools": { + "Package": "gtools", + "Version": "3.9.5", + "Source": "Repository", + "Title": "Various R Programming Tools", + "Description": "Functions to assist in R programming, including: - assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse logit transformations ('logit', 'inv.logit'), - test if a value is missing, empty or contains only NA and NULL values ('invalid'), - manipulate R's .Last function ('addLast'), - define macros ('defmacro'), - detect odd and even integers ('odd', 'even'), - convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a binary search ('binsearch'), - sort strings containing both numeric and character components ('mixedsort'), - create a factor variable from the quantiles of a continuous variable ('quantcut'), - enumerate permutations and combinations ('combinations', 'permutation'), - calculate and convert between fold-change and log-ratio ('foldchange', 'logratio2foldchange', 'foldchange2logratio'), - calculate probabilities and generate random numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet'), - apply a function over adjacent subsets of a vector ('running'), - modify the TCP_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of data frames, even if the column names don't match ('smartbind'), - generate significance stars from p-values ('stars.pval'), - convert characters to/from ASCII codes ('asc', 'chr'), - convert character vector to ASCII representation ('ASCIIfy'), - apply title capitalization rules to a character vector ('capwords').", + "Authors@R": "c(person(\"Gregory R.\", \"Warnes\", role = \"aut\"), person(\"Ben\", \"Bolker\", role = c(\"aut\", \"cre\"), email = \"bolker@mcmaster.ca\", comment=c(ORCID=\"0000-0002-2127-0443\")), person(\"Thomas\", \"Lumley\", role = \"aut\"), person(\"Arni\", \"Magnusson\", role = \"aut\"), person(\"Bill\", \"Venables\", role = \"aut\"), person(\"Genei\", \"Ryodan\", role = \"aut\"), person(\"Steffen\", \"Moeller\", role = \"aut\"), person(\"Ian\", \"Wilson\", role = \"ctb\"), person(\"Mark\", \"Davis\", role = \"ctb\"), person(\"Nitin\", \"Jain\", role=\"ctb\"), person(\"Scott\", \"Chamberlain\", role = \"ctb\"))", + "License": "GPL-2", + "Depends": [ + "methods", + "stats", + "utils" + ], + "URL": "https://github.com/r-gregmisc/gtools", + "BugReports": "https://github.com/r-gregmisc/gtools/issues", + "Language": "en-US", + "Suggests": [ + "car", + "gplots", + "knitr", + "rstudioapi", + "SGP", + "taxize" + ], + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Gregory R. Warnes [aut], Ben Bolker [aut, cre] (), Thomas Lumley [aut], Arni Magnusson [aut], Bill Venables [aut], Genei Ryodan [aut], Steffen Moeller [aut], Ian Wilson [ctb], Mark Davis [ctb], Nitin Jain [ctb], Scott Chamberlain [ctb]", + "Maintainer": "Ben Bolker ", + "Repository": "CRAN" + }, + "haven": { + "Package": "haven", + "Version": "2.5.5", + "Source": "Repository", + "Title": "Import and Export 'SPSS', 'Stata' and 'SAS' Files", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Evan\", \"Miller\", role = c(\"aut\", \"cph\"), comment = \"Author of included ReadStat code\"), person(\"Danny\", \"Smith\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Import foreign statistical formats into R via the embedded 'ReadStat' C library, .", + "License": "MIT + file LICENSE", + "URL": "https://haven.tidyverse.org, https://github.com/tidyverse/haven, https://github.com/WizardMac/ReadStat", + "BugReports": "https://github.com/tidyverse/haven/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.0.0)", + "forcats (>= 0.2.0)", + "hms", + "lifecycle", + "methods", + "readr (>= 0.1.0)", + "rlang (>= 0.4.0)", + "tibble", + "tidyselect", + "vctrs (>= 0.3.0)" + ], + "Suggests": [ + "covr", + "crayon", + "fs", + "knitr", + "pillar (>= 1.4.0)", + "rmarkdown", + "testthat (>= 3.0.0)", + "utf8" + ], + "LinkingTo": [ + "cpp11" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "SystemRequirements": "GNU make, zlib: zlib1g-dev (deb), zlib-devel (rpm)", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], Evan Miller [aut, cph] (Author of included ReadStat code), Danny Smith [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "here": { + "Package": "here", + "Version": "1.0.1", + "Source": "Repository", + "Title": "A Simpler Way to Find Your Files", + "Date": "2020-12-13", + "Authors@R": "c(person(given = \"Kirill\", family = \"M\\u00fcller\", role = c(\"aut\", \"cre\"), email = \"krlmlr+r@mailbox.org\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Jennifer\", family = \"Bryan\", role = \"ctb\", email = \"jenny@rstudio.com\", comment = c(ORCID = \"0000-0002-6983-2759\")))", + "Description": "Constructs paths to your project's files. Declare the relative path of a file within your project with 'i_am()'. Use the 'here()' function as a drop-in replacement for 'file.path()', it will always locate the files relative to your project root.", + "License": "MIT + file LICENSE", + "URL": "https://here.r-lib.org/, https://github.com/r-lib/here", + "BugReports": "https://github.com/r-lib/here/issues", + "Imports": [ + "rprojroot (>= 2.0.2)" + ], + "Suggests": [ + "conflicted", + "covr", + "fs", + "knitr", + "palmerpenguins", + "plyr", + "readr", + "rlang", + "rmarkdown", + "testthat", + "uuid", + "withr" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.1.1.9000", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Kirill Müller [aut, cre] (), Jennifer Bryan [ctb] ()", + "Maintainer": "Kirill Müller ", + "Repository": "CRAN" + }, + "highr": { + "Package": "highr", + "Version": "0.11", + "Source": "Repository", + "Type": "Package", + "Title": "Syntax Highlighting for R Source Code", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Yixuan\", \"Qiu\", role = \"aut\"), person(\"Christopher\", \"Gandrud\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\") )", + "Description": "Provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package ().", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "xfun (>= 0.18)" + ], + "Suggests": [ + "knitr", + "markdown", + "testit" + ], + "License": "GPL", + "URL": "https://github.com/yihui/highr", + "BugReports": "https://github.com/yihui/highr/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (), Yixuan Qiu [aut], Christopher Gandrud [ctb], Qiang Li [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "hms": { + "Package": "hms", + "Version": "1.1.3", + "Source": "Repository", + "Title": "Pretty Time of Day", + "Date": "2023-03-21", + "Authors@R": "c( person(\"Kirill\", \"Müller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\"), person(\"RStudio\", role = \"fnd\") )", + "Description": 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"Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Barret\", \"Schloerke\", , \"barret@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Yihui\", \"Xie\", , \"yihui@posit.co\", role = \"aut\"), person(\"Jeff\", \"Allen\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Tools for HTML generation and output.", + "License": "GPL (>= 2)", + "URL": "https://github.com/rstudio/htmltools, https://rstudio.github.io/htmltools/", + "BugReports": "https://github.com/rstudio/htmltools/issues", + "Depends": [ + "R (>= 2.14.1)" + ], + "Imports": [ + "base64enc", + "digest", + "fastmap (>= 1.1.0)", + "grDevices", + "rlang (>= 1.0.0)", 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person(\"Yihui\", \"Xie\", role = \"aut\"), person(\"JJ\", \"Allaire\", role = \"aut\"), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Kenton\", \"Russell\", role = c(\"aut\", \"cph\")), person(\"Ellis\", \"Hughes\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/ramnathv/htmlwidgets", + "BugReports": "https://github.com/ramnathv/htmlwidgets/issues", + "Imports": [ + "grDevices", + "htmltools (>= 0.5.7)", + "jsonlite (>= 0.9.16)", + "knitr (>= 1.8)", + "rmarkdown", + "yaml" + ], + "Suggests": [ + "testthat" + ], + "Enhances": [ + "shiny (>= 1.1)" + ], + 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\"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Emergya (Cloud4all, FP7/2007-2013, grant agreement no 289016)\", role = \"cph\", comment = \"libuv subcomponent: android-ifaddrs.h, android-ifaddrs.c\"), person(\"Steve\", \"Reid\", role = \"aut\", comment = \"SHA-1 implementation\"), person(\"James\", \"Brown\", role = \"aut\", comment = \"SHA-1 implementation\"), person(\"Bob\", \"Trower\", role = \"aut\", comment = \"base64 implementation\"), person(\"Alexander\", \"Peslyak\", role = \"aut\", comment = \"MD5 implementation\"), person(\"Trantor Standard Systems\", role = \"cph\", comment = \"base64 implementation\"), person(\"Igor\", \"Sysoev\", role = \"cph\", comment = \"http-parser\") )", + "Description": "Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. 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The functions are scheduled in an event loop.", + "URL": "https://r-lib.github.io/later/, https://github.com/r-lib/later", + "BugReports": "https://github.com/r-lib/later/issues", + "License": "MIT + file LICENSE", + "Imports": [ + "Rcpp (>= 0.12.9)", + "rlang" + ], + "LinkingTo": [ + "Rcpp" + ], + "RoxygenNote": "7.3.2", + "Suggests": [ + "knitr", + "nanonext", + "R6", + "rmarkdown", + "testthat (>= 2.1.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Winston Chang [aut, cre], Joe Cheng [aut], Charlie Gao [aut] (), Posit Software, PBC [cph], Marcus Geelnard [ctb, cph] (TinyCThread library, https://tinycthread.github.io/), Evan Nemerson [ctb, cph] (TinyCThread library, https://tinycthread.github.io/)", + "Maintainer": "Winston Chang ", + "Repository": "CRAN" + }, + "lattice": { + "Package": "lattice", + "Version": "0.22-6", + "Source": "Repository", + "Date": "2024-03-20", + "Priority": "recommended", + "Title": "Trellis Graphics for R", + "Authors@R": "c(person(\"Deepayan\", \"Sarkar\", role = c(\"aut\", \"cre\"), email = \"deepayan.sarkar@r-project.org\", comment = c(ORCID = \"0000-0003-4107-1553\")), person(\"Felix\", \"Andrews\", role = \"ctb\"), person(\"Kevin\", \"Wright\", role = \"ctb\", comment = \"documentation\"), person(\"Neil\", \"Klepeis\", role = \"ctb\"), person(\"Johan\", \"Larsson\", role = \"ctb\", comment = \"miscellaneous improvements\"), person(\"Zhijian (Jason)\", \"Wen\", role = \"cph\", comment = \"filled contour code\"), person(\"Paul\", \"Murrell\", role = \"ctb\", email = \"paul@stat.auckland.ac.nz\"), person(\"Stefan\", \"Eng\", role = \"ctb\", comment = \"violin plot improvements\"), person(\"Achim\", \"Zeileis\", role = \"ctb\", comment = \"modern colors\"), person(\"Alexandre\", \"Courtiol\", role = \"ctb\", comment = \"generics for larrows, lpolygon, lrect and lsegments\") )", + "Description": "A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. 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For instance, the elements of a list environment are ordered and can be accessed and iterated over using index subsetting, e.g. 'x <- listenv(a = 1, b = 2); for (i in seq_along(x)) x[[i]] <- x[[i]] ^ 2; y <- as.list(x)'.", + "License": "LGPL (>= 2.1)", + "LazyLoad": "TRUE", + "URL": "https://listenv.futureverse.org, https://github.com/HenrikBengtsson/listenv", + "BugReports": "https://github.com/HenrikBengtsson/listenv/issues", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Henrik Bengtsson [aut, cre, cph]", + "Maintainer": "Henrik Bengtsson ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "lmtest": { + "Package": "lmtest", + "Version": "0.9-40", + "Source": "Repository", + "Title": "Testing Linear Regression Models", + "Date": "2022-03-21", + "Authors@R": "c(person(given = \"Torsten\", family = \"Hothorn\", role = \"aut\", email = \"Torsten.Hothorn@R-project.org\", comment = c(ORCID = \"0000-0001-8301-0471\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = c(\"Richard\", \"W.\"), family = \"Farebrother\", role = \"aut\", comment = \"pan.f\"), person(given = \"Clint\", family = \"Cummins\", role = \"aut\", comment = \"pan.f\"), person(given = \"Giovanni\", family = \"Millo\", role = \"ctb\"), person(given = \"David\", family = \"Mitchell\", role = \"ctb\"))", + "Description": "A collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.", + "LazyData": "yes", + "Depends": [ + "R (>= 3.0.0)", + "stats", + "zoo" + ], + "Suggests": [ + "car", + "strucchange", + "sandwich", + "dynlm", + "stats4", + "survival", + "AER" + ], + "Imports": [ + "graphics" + ], + "License": "GPL-2 | GPL-3", + "NeedsCompilation": "yes", + "Author": "Torsten Hothorn [aut] (), Achim Zeileis [aut, cre] (), Richard W. Farebrother [aut] (pan.f), Clint Cummins [aut] (pan.f), Giovanni Millo [ctb], David Mitchell [ctb]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "lubridate": { + "Package": "lubridate", + "Version": "1.9.4", + "Source": "Repository", + "Type": "Package", + "Title": "Make Dealing with Dates a Little Easier", + "Authors@R": "c( person(\"Vitalie\", \"Spinu\", , \"spinuvit@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Garrett\", \"Grolemund\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Davis\", \"Vaughan\", role = \"ctb\"), person(\"Ian\", \"Lyttle\", role = \"ctb\"), person(\"Imanuel\", \"Costigan\", role = \"ctb\"), person(\"Jason\", \"Law\", role = \"ctb\"), person(\"Doug\", \"Mitarotonda\", role = \"ctb\"), person(\"Joseph\", \"Larmarange\", role = \"ctb\"), person(\"Jonathan\", \"Boiser\", role = \"ctb\"), person(\"Chel Hee\", \"Lee\", role = \"ctb\") )", + "Maintainer": "Vitalie Spinu ", + "Description": "Functions to work with date-times and time-spans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and time-span objects. 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person(\"Robert\", \"Lamb\", role=\"ctb\"), person(\"NA\", \"Laskurain\", role=\"ctb\"), person(\"George\", \"Leser\", role=\"ctb\"), person(\"Marie-Colette\", \"van Lieshout\", role=\"ctb\"), person(\"AF\", \"Mark\", role=\"ctb\"), person(\"Sebastian\", \"Meyer\", role=\"ctb\"), person(\"Jorge\", \"Mateu\", role=\"ctb\"), person(\"Annikki\", \"Makela\", role=\"ctb\"), person(\"Enrique\", \"Miranda\", role=\"ctb\"), person(\"Nicoletta\", \"Nava\", role=\"ctb\"), person(\"M\", \"Numata\", role=\"ctb\"), person(\"Matti\", \"Nummelin\", role=\"ctb\"), person(\"Jens Randel\", \"Nyengaard\", role=\"ctb\"), person(\"Yosihiko\", \"Ogata\", role=\"ctb\"), person(\"Si\", \"Palmer\", role=\"ctb\"), person(\"Antti\", \"Penttinen\", role=\"ctb\"), person(\"Sandra\", \"Pereira\", role=\"ctb\"), person(\"Nicolas\", \"Picard\", role=\"ctb\"), person(\"William\", \"Platt\", role=\"ctb\"), person(\"Stephen\", \"Rathbun\", role=\"ctb\"), person(\"Brian\", \"Ripley\", role=\"ctb\"), person(\"Roger\", \"Sainsbury\", role=\"ctb\"), person(\"Dietrich\", \"Stoyan\", role=\"ctb\"), person(\"David\", \"Strauss\", role=\"ctb\"), person(\"L\", \"Strand\", role=\"ctb\"), person(\"Masaharu\", \"Tanemura\", role=\"ctb\"), person(\"Graham\", \"Upton\", role=\"ctb\"), person(\"Bill\", \"Venables\", role=\"ctb\"), person(\"Ulrich\", \"Vogel\", role=\"ctb\"), person(\"Sasha\", \"Voss\", role=\"ctb\"), person(\"Rasmus\", \"Waagepetersen\", role=\"ctb\"), person(\"Keith\", \"Watkins\", role=\"ctb\"), person(\"H\", \"Wendrock\", role=\"ctb\") )", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "spatstat.utils (>= 3.1-2)", + "Matrix" + ], + "Suggests": [ + "spatstat.geom", + "spatstat.random", + "spatstat.explore", + "spatstat.model", + "spatstat.linnet" + ], + "Description": "Contains all the datasets for the 'spatstat' family of packages.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "LazyData": "true", + "NeedsCompilation": "no", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.data/issues", + "Author": "Adrian Baddeley [aut, cre] (), Rolf Turner [aut] (), Ege Rubak [aut] (), W Aherne [ctb], Freda Alexander [ctb], Qi Wei Ang [ctb], Sourav Banerjee [ctb], Mark Berman [ctb], R Bernhardt [ctb], Thomas Berndtsen [ctb], Andrew Bevan [ctb], Jeffrey Betts [ctb], Ray Cartwright [ctb], Lucia Cobo Sanchez [ctb], Richard Condit [ctb], Francis Crick [ctb], Marcelino de la Cruz Rot [ctb], Jack Cuzick [ctb], Tilman Davies [ctb], Peter Diggle [ctb], Michael Drinkwater [ctb], Stephen Eglen [ctb], Robert Edwards [ctb], Johannes Elias [ctb], AE Esler [ctb], Gregory Evans [ctb], Bernard Fingleton [ctb], Olivier Flores [ctb], David Ford [ctb], Robin Foster [ctb], Janet Franklin [ctb], Neba Funwi-Gabga [ctb], DJ Gerrard [ctb], Andy Green [ctb], Tim Griffin [ctb], Ute Hahn [ctb], RD Harkness [ctb], Arthur Hickman [ctb], Stephen Hubbell [ctb], Austin Hughes [ctb], Jonathan Huntington [ctb], MJ Hutchings [ctb], Jackie Inwald [ctb], Valerie Isham [ctb], Aruna Jammalamadaka [ctb], Carl Knox-Robinson [ctb], Mahdieh Khanmohammadi [ctb], Tero Kokkila [ctb], Bas Kooijman [ctb], Kenneth Kosik [ctb], Peter Kovesi [ctb], Lily Kozmian-Ledward [ctb], Robert Lamb [ctb], NA Laskurain [ctb], George Leser [ctb], Marie-Colette van Lieshout [ctb], AF Mark [ctb], Sebastian Meyer [ctb], Jorge Mateu [ctb], Annikki Makela [ctb], Enrique Miranda [ctb], Nicoletta Nava [ctb], M Numata [ctb], Matti Nummelin [ctb], Jens Randel Nyengaard [ctb], Yosihiko Ogata [ctb], Si Palmer [ctb], Antti Penttinen [ctb], Sandra Pereira [ctb], Nicolas Picard [ctb], William Platt [ctb], Stephen Rathbun [ctb], Brian Ripley [ctb], Roger Sainsbury [ctb], Dietrich Stoyan [ctb], David Strauss [ctb], L Strand [ctb], Masaharu Tanemura [ctb], Graham Upton [ctb], Bill Venables [ctb], Ulrich Vogel [ctb], Sasha Voss [ctb], Rasmus Waagepetersen [ctb], Keith Watkins [ctb], H Wendrock [ctb]", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "spatstat.explore": { + "Package": "spatstat.explore", + "Version": "3.4-3", + "Source": "Repository", + "Date": "2025-05-21", + "Title": "Exploratory Data Analysis for the 'spatstat' Family", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Kasper\", \"Klitgaard Berthelsen\", role = \"ctb\"), person(\"Warick\", \"Brown\", role = \"cph\"), person(\"Achmad\", \"Choiruddin\", role = \"ctb\"), person(\"Ya-Mei\", \"Chang\", role = \"ctb\"), person(\"Jean-Francois\", \"Coeurjolly\", role = \"ctb\"), person(\"Ottmar\", \"Cronie\", role = \"ctb\"), person(\"Tilman\", \"Davies\", role = c(\"ctb\", \"cph\")), person(\"Julian\", \"Gilbey\", role = \"ctb\"), person(\"Jonatan\", \"Gonzalez\", role = \"ctb\"), person(\"Yongtao\", \"Guan\", role = \"ctb\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Martin\", \"Hazelton\", role = \"ctb\"), person(\"Kassel\", \"Hingee\", role = c(\"ctb\", \"cph\")), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Frederic\", \"Lavancier\", role = \"ctb\"), person(\"Marie-Colette\", \"van Lieshout\", role = c(\"ctb\", \"cph\")), person(\"Greg\", \"McSwiggan\", role = \"ctb\"), person(\"Robin K\", \"Milne\", role = \"cph\"), person(\"Tuomas\", \"Rajala\", role = \"ctb\"), person(\"Suman\", \"Rakshit\", role = c(\"ctb\", \"cph\")), person(\"Dominic\", \"Schuhmacher\", role = \"ctb\"), person(\"Rasmus\", \"Plenge Waagepetersen\", role = \"ctb\"), person(\"Hangsheng\", \"Wang\", role = \"ctb\"), person(\"Tingting\", \"Zhan\", role=\"ctb\"))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "spatstat.data (>= 3.1-2)", + "spatstat.univar (>= 3.1-2)", + "spatstat.geom (>= 3.3-6)", + "spatstat.random (>= 3.3-2)", + "stats", + "graphics", + "grDevices", + "utils", + "methods", + "nlme" + ], + "Imports": [ + "spatstat.utils (>= 3.1-0)", + "spatstat.sparse (>= 3.1-0)", + "goftest (>= 1.2-2)", + "Matrix", + "abind" + ], + "Suggests": [ + "sm", + "gsl", + "locfit", + "spatial", + "fftwtools (>= 0.9-8)", + "spatstat.linnet (>= 3.2-1)", + "spatstat.model (>= 3.3-1)", + "spatstat (>= 3.1-1)" + ], + "Description": "Functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.explore/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Kasper Klitgaard Berthelsen [ctb], Warick Brown [cph], Achmad Choiruddin [ctb], Ya-Mei Chang [ctb], Jean-Francois Coeurjolly [ctb], Ottmar Cronie [ctb], Tilman Davies [ctb, cph], Julian Gilbey [ctb], Jonatan Gonzalez [ctb], Yongtao Guan [ctb], Ute Hahn [ctb], Martin Hazelton [ctb], Kassel Hingee [ctb, cph], Abdollah Jalilian [ctb], Frederic Lavancier [ctb], Marie-Colette van Lieshout [ctb, cph], Greg McSwiggan [ctb], Robin K Milne [cph], Tuomas Rajala [ctb], Suman Rakshit [ctb, cph], Dominic Schuhmacher [ctb], Rasmus Plenge Waagepetersen [ctb], Hangsheng Wang [ctb], Tingting Zhan [ctb]", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "spatstat.geom": { + "Package": "spatstat.geom", + "Version": "3.4-1", + "Source": "Repository", + "Date": "2025-05-20", + "Title": "Geometrical Functionality of the 'spatstat' Family", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Warick\", \"Brown\" , role = \"ctb\"), person(\"Tilman\", \"Davies\", role = \"ctb\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Martin\", \"Hazelton\", role = \"ctb\"), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Greg\", \"McSwiggan\", role = c(\"ctb\", \"cph\")), person(\"Sebastian\", \"Meyer\", role = c(\"ctb\", \"cph\")), person(\"Jens\", \"Oehlschlaegel\", role = c(\"ctb\", \"cph\")), person(\"Suman\", \"Rakshit\", role = \"ctb\"), person(\"Dominic\", \"Schuhmacher\", role = \"ctb\"), person(\"Rasmus\", \"Waagepetersen\", role = \"ctb\"))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "spatstat.data (>= 3.1)", + "spatstat.univar (>= 3.1)", + "stats", + "graphics", + "grDevices", + "utils", + "methods" + ], + "Imports": [ + "spatstat.utils (>= 3.1-4)", + "deldir (>= 1.0-2)", + "polyclip (>= 1.10)" + ], + "Suggests": [ + "spatstat.random (>= 3.3)", + "spatstat.explore (>= 3.3)", + "spatstat.model (>= 3.3)", + "spatstat.linnet (>= 3.2)", + "spatial", + "fftwtools (>= 0.9-8)", + "spatstat (>= 3.3)" + ], + "Description": "Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.geom/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Warick Brown [ctb], Tilman Davies [ctb], Ute Hahn [ctb], Martin Hazelton [ctb], Abdollah Jalilian [ctb], Greg McSwiggan [ctb, cph], Sebastian Meyer [ctb, cph], Jens Oehlschlaegel [ctb, cph], Suman Rakshit [ctb], Dominic Schuhmacher [ctb], Rasmus Waagepetersen [ctb]", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "spatstat.random": { + "Package": "spatstat.random", + "Version": "3.4-1", + "Source": "Repository", + "Date": "2025-05-20", + "Title": "Random Generation Functionality for the 'spatstat' Family", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Tilman\", \"Davies\", role = c(\"aut\", \"cph\"), comment=c(ORCID=\"0000-0003-0565-1825\")), person(\"Kasper\", \"Klitgaard Berthelsen\", role = c(\"ctb\", \"cph\")), person(\"David\", \"Bryant\", role = c(\"ctb\", \"cph\")), person(\"Ya-Mei\", \"Chang\", role = c(\"ctb\", \"cph\"), email = \"yamei628@gmail.com\"), person(\"Ute\", \"Hahn\", role = \"ctb\"), person(\"Abdollah\", \"Jalilian\", role = \"ctb\"), person(\"Dominic\", \"Schuhmacher\", role = c(\"ctb\", \"cph\")), person(\"Rasmus\", \"Plenge Waagepetersen\", role = c(\"ctb\", \"cph\")))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "spatstat.data (>= 3.1)", + "spatstat.univar (>= 3.1)", + "spatstat.geom (>= 3.3-6)", + "stats", + "utils", + "methods", + "grDevices" + ], + "Imports": [ + "spatstat.utils (>= 3.1-4)" + ], + "Suggests": [ + "spatial", + "spatstat.linnet (>= 3.2)", + "spatstat.explore", + "spatstat.model", + "spatstat (>= 3.3)", + "gsl" + ], + "Description": "Functionality for random generation of spatial data in the 'spatstat' family of packages. Generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes including simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes (using direct, Brix-Kendall, or hybrid algorithms), log-Gaussian Cox processes, product shot noise cluster processes and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler, or coupling-from-the-past perfect simulation). Also generates random spatial patterns of line segments, random tessellations, and random images (random noise, random mosaics). Excludes random generation on a linear network, which is covered by the separate package 'spatstat.linnet'.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.random/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Tilman Davies [aut, cph] (ORCID: ), Kasper Klitgaard Berthelsen [ctb, cph], David Bryant [ctb, cph], Ya-Mei Chang [ctb, cph], Ute Hahn [ctb], Abdollah Jalilian [ctb], Dominic Schuhmacher [ctb, cph], Rasmus Plenge Waagepetersen [ctb, cph]", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "spatstat.sparse": { + "Package": "spatstat.sparse", + "Version": "3.1-0", + "Source": "Repository", + "Date": "2024-06-21", + "Title": "Sparse Three-Dimensional Arrays and Linear Algebra Utilities", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "stats", + "utils", + "methods", + "Matrix", + "abind", + "tensor" + ], + "Imports": [ + "spatstat.utils (>= 3.0-5)" + ], + "Description": "Defines sparse three-dimensional arrays and supports standard operations on them. The package also includes utility functions for matrix calculations that are common in statistics, such as quadratic forms.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.sparse/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (), Rolf Turner [aut, cph] (), Ege Rubak [aut, cph] ()", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "spatstat.univar": { + "Package": "spatstat.univar", + "Version": "3.1-4", + "Source": "Repository", + "Date": "2025-07-13", + "Title": "One-Dimensional Probability Distribution Support for the 'spatstat' Family", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(c(\"Tilman\", \"M.\"), \"Davies\", role = c(\"aut\", \"ctb\", \"cph\"), email = \"Tilman.Davies@otago.ac.nz\", comment = c(ORCID=\"0000-0003-0565-1825\")), person(c(\"Martin\", \"L.\"), \"Hazelton\", role = c(\"aut\", \"ctb\", \"cph\"), email = \"Martin.Hazelton@otago.ac.nz\", comment = c(ORCID=\"0000-0001-7831-725X\")), person(\"Ege\", \"Rubak\", role = c(\"aut\", \"cph\"), email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")), person(\"Rolf\", \"Turner\", role = c(\"aut\", \"cph\"), email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Greg\", \"McSwiggan\", role = c(\"ctb\", \"cph\")))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "stats" + ], + "Imports": [ + "spatstat.utils (>= 3.1-2)", + "graphics" + ], + "Description": "Estimation of one-dimensional probability distributions including kernel density estimation, weighted empirical cumulative distribution functions, Kaplan-Meier and reduced-sample estimators for right-censored data, heat kernels, kernel properties, quantiles and integration.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.univar/issues", + "Author": "Adrian Baddeley [aut, cre, cph] (ORCID: ), Tilman M. Davies [aut, ctb, cph] (ORCID: ), Martin L. Hazelton [aut, ctb, cph] (ORCID: ), Ege Rubak [aut, cph] (ORCID: ), Rolf Turner [aut, cph] (ORCID: ), Greg McSwiggan [ctb, cph]", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "spatstat.utils": { + "Package": "spatstat.utils", + "Version": "3.1-4", + "Source": "Repository", + "Date": "2025-05-15", + "Title": "Utility Functions for 'spatstat'", + "Authors@R": "c(person(\"Adrian\", \"Baddeley\", role = c(\"aut\", \"cre\"), email = \"Adrian.Baddeley@curtin.edu.au\", comment = c(ORCID=\"0000-0001-9499-8382\")), person(\"Rolf\", \"Turner\", role = \"aut\", email=\"rolfturner@posteo.net\", comment=c(ORCID=\"0000-0001-5521-5218\")), person(\"Ege\", \"Rubak\", role = \"aut\", email = \"rubak@math.aau.dk\", comment=c(ORCID=\"0000-0002-6675-533X\")))", + "Maintainer": "Adrian Baddeley ", + "Depends": [ + "R (>= 3.5.0)", + "stats", + "graphics", + "grDevices", + "utils", + "methods" + ], + "Suggests": [ + "spatstat.model" + ], + "Description": "Contains utility functions for the 'spatstat' family of packages which may also be useful for other purposes.", + "License": "GPL (>= 2)", + "URL": "http://spatstat.org/", + "NeedsCompilation": "yes", + "ByteCompile": "true", + "BugReports": "https://github.com/spatstat/spatstat.utils/issues", + "Author": "Adrian Baddeley [aut, cre] (ORCID: ), Rolf Turner [aut] (ORCID: ), Ege Rubak [aut] (ORCID: )", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "stringi": { + "Package": "stringi", + "Version": "1.8.7", + "Source": "Repository", + "Date": "2025-03-27", + "Title": "Fast and Portable Character String Processing Facilities", + "Description": "A collection of character string/text/natural language processing tools for pattern searching (e.g., with 'Java'-like regular expressions or the 'Unicode' collation algorithm), random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date-time formatting and parsing, and many more. They are fast, consistent, convenient, and - thanks to 'ICU' (International Components for Unicode) - portable across all locales and platforms. 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This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.", + "Imports": [ + "xfun (>= 0.48)" + ], + "Suggests": [ + "testit", + "rstudioapi" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/tinytex", + "BugReports": "https://github.com/rstudio/tinytex/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre, cph] (), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (), Devon Ryan [ctb] (), Ethan Heinzen [ctb], Fernando Cagua [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.5.0", + "Source": "Repository", + "Title": "Time Zone Database Information", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Howard\", \"Hinnant\", role = \"cph\", comment = \"Author of the included date library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the 'date' library. 'date' provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.", + "License": "MIT + file LICENSE", + "URL": "https://tzdb.r-lib.org, https://github.com/r-lib/tzdb", + "BugReports": "https://github.com/r-lib/tzdb/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.5.2)" + ], + "Biarch": "yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Howard Hinnant [cph] (Author of the included date library), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "usethis": { + "Package": "usethis", + "Version": "3.1.0", + "Source": "Repository", + "Title": "Automate Package and Project Setup", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Malcolm\", \"Barrett\", , \"malcolmbarrett@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0003-0299-5825\")), person(\"Andy\", \"Teucher\", , \"andy.teucher@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-7840-692X\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.", + "License": "MIT + file LICENSE", + "URL": "https://usethis.r-lib.org, https://github.com/r-lib/usethis", + "BugReports": "https://github.com/r-lib/usethis/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.0.1)", + "clipr (>= 0.3.0)", + "crayon", + "curl (>= 2.7)", + "desc (>= 1.4.2)", + "fs (>= 1.3.0)", + "gert (>= 1.4.1)", + "gh (>= 1.2.1)", + "glue (>= 1.3.0)", + "jsonlite", + "lifecycle (>= 1.0.0)", + "purrr", + "rappdirs", + "rlang (>= 1.1.0)", + "rprojroot (>= 1.2)", + "rstudioapi", + "stats", + "tools", + "utils", + "whisker", + "withr (>= 2.3.0)", + "yaml" + ], + "Suggests": [ + "covr", + "knitr", + "magick", + "pkgload (>= 1.3.2.1)", + "rmarkdown", + "roxygen2 (>= 7.1.2)", + "spelling (>= 1.2)", + "styler (>= 1.2.0)", + "testthat (>= 3.1.8)" + ], + "Config/Needs/website": "r-lib/asciicast, tidyverse/tidytemplate, xml2", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "TRUE", + "Config/testthat/start-first": "github-actions, release", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut] (), Jennifer Bryan [aut, cre] (), Malcolm Barrett [aut] (), Andy Teucher [aut] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.6", + "Source": "Repository", + "Title": "Unicode Text Processing", + "Authors@R": "c(person(given = c(\"Patrick\", \"O.\"), family = \"Perry\", role = c(\"aut\", \"cph\")), person(given = \"Kirill\", family = \"M\\u00fcller\", role = \"cre\", email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Unicode, Inc.\", role = c(\"cph\", \"dtc\"), comment = \"Unicode Character Database\"))", + "Description": "Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.", + "License": "Apache License (== 2.0) | file LICENSE", + "URL": "https://krlmlr.github.io/utf8/, https://github.com/krlmlr/utf8", + "BugReports": "https://github.com/krlmlr/utf8/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "cli", + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr, rmarkdown", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2.9000", + "NeedsCompilation": "yes", + "Author": "Patrick O. Perry [aut, cph], Kirill Müller [cre] (ORCID: ), Unicode, Inc. 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(2018) . It also provides means to transform new data and to carry out supervised dimensionality reduction. An implementation of the related LargeVis method of Tang et al. (2016) is also provided. This is a complete re-implementation in R (and C++, via the 'Rcpp' package): no Python installation is required. See the uwot website () for more documentation and examples.", + "License": "GPL (>= 3)", + "URL": "https://github.com/jlmelville/uwot, https://jlmelville.github.io/uwot/", + "BugReports": "https://github.com/jlmelville/uwot/issues", + "Depends": [ + "Matrix" + ], + "Imports": [ + "FNN", + "irlba", + "methods", + "Rcpp", + "RcppAnnoy (>= 0.0.17)", + "RSpectra" + ], + "Suggests": [ + "bigstatsr", + "covr", + "knitr", + "RcppHNSW", + "rmarkdown", + "rnndescent", + "testthat" + ], + "LinkingTo": [ + "dqrng", + "Rcpp", + "RcppAnnoy", + "RcppProgress" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "rmarkdown", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "James Melville [aut, cre, cph], Aaron Lun [ctb], Mohamed Nadhir Djekidel [ctb], Yuhan Hao [ctb], Dirk Eddelbuettel [ctb], Wouter van der Bijl [ctb]", + "Maintainer": "James Melville ", + "Repository": "CRAN" + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.6.5", + "Source": "Repository", + "Title": "Vector Helpers", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"aut\"), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"data.table team\", role = \"cph\", comment = \"Radix sort based on data.table's forder() and their contribution to R's order()\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analysing function interfaces.", + "License": "MIT + file LICENSE", + "URL": "https://vctrs.r-lib.org/, https://github.com/r-lib/vctrs", + "BugReports": "https://github.com/r-lib/vctrs/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "glue", + "lifecycle (>= 1.0.3)", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "bit64", + "covr", + "crayon", + "dplyr (>= 0.8.5)", + "generics", + "knitr", + "pillar (>= 1.4.4)", + "pkgdown (>= 2.0.1)", + "rmarkdown", + "testthat (>= 3.0.0)", + "tibble (>= 3.1.3)", + "waldo (>= 0.2.0)", + "withr", + "xml2", + "zeallot" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-GB", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Lionel Henry [aut], Davis Vaughan [aut, cre], data.table team [cph] (Radix sort based on data.table's forder() and their contribution to R's order()), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "viridis": { + "Package": "viridis", + "Version": "0.6.5", + "Source": "Repository", + "Type": "Package", + "Title": "Colorblind-Friendly Color Maps for R", + "Date": "2024-01-28", + "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )", + "Maintainer": "Simon Garnier ", + "Description": "Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This package also contains 'ggplot2' bindings for discrete and continuous color and fill scales. A lean version of the package called 'viridisLite' that does not include the 'ggplot2' bindings can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)", + "viridisLite (>= 0.4.0)" + ], + "Imports": [ + "ggplot2 (>= 1.0.1)", + "gridExtra" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "scales", + "MASS", + "knitr", + "dichromat", + "colorspace", + "httr", + "mapproj", + "vdiffr", + "svglite (>= 1.2.0)", + "testthat", + "covr", + "rmarkdown", + "maps", + "terra" + ], + "LazyData": "true", + "VignetteBuilder": "knitr", + "URL": "https://sjmgarnier.github.io/viridis/, https://github.com/sjmgarnier/viridis/", + "BugReports": "https://github.com/sjmgarnier/viridis/issues", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.2", + "Source": "Repository", + "Type": "Package", + "Title": "Colorblind-Friendly Color Maps (Lite Version)", + "Date": "2023-05-02", + "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )", + "Maintainer": "Simon Garnier ", + "Description": "Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "ggplot2 (>= 1.0.1)", + "testthat", + "covr" + ], + "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", + "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" + }, + "vroom": { + "Package": "vroom", + "Version": "1.6.5", + "Source": "Repository", + "Title": "Read and Write Rectangular Text Data Quickly", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. 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Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.10", + "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Date": "2024-07-22", + "Suggests": [ + "RUnit" + ], + "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", + "Maintainer": "Shawn Garbett ", + "License": "BSD_3_clause + file LICENSE", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "URL": "https://github.com/vubiostat/r-yaml/", + "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN" + }, + "zip": { + "Package": "zip", + "Version": "2.3.3", + "Source": "Repository", + "Title": "Cross-Platform 'zip' Compression", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kuba\", \"Podgórski\", role = \"ctb\"), person(\"Rich\", \"Geldreich\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/zip, https://r-lib.github.io/zip/", + "BugReports": "https://github.com/r-lib/zip/issues", + "Suggests": [ + "covr", + "pillar", + "processx", + "R6", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-05-07", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2.9000", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Kuba Podgórski [ctb], Rich Geldreich [ctb], Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "zoo": { + "Package": "zoo", + "Version": "1.8-14", + "Source": "Repository", + "Date": "2025-04-09", + "Title": "S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Gabor\", family = \"Grothendieck\", role = \"aut\", email = \"ggrothendieck@gmail.com\"), person(given = c(\"Jeffrey\", \"A.\"), family = \"Ryan\", role = \"aut\", email = \"jeff.a.ryan@gmail.com\"), person(given = c(\"Joshua\", \"M.\"), family = \"Ulrich\", role = \"ctb\", email = \"josh.m.ulrich@gmail.com\"), person(given = \"Felix\", family = \"Andrews\", role = \"ctb\", email = \"felix@nfrac.org\"))", + "Description": "An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.", + "Depends": [ + "R (>= 3.1.0)", + "stats" + ], + "Suggests": [ + "AER", + "coda", + "chron", + "ggplot2 (>= 3.5.0)", + "mondate", + "scales", + "stinepack", + "strucchange", + "timeDate", + "timeSeries", + "tinyplot", + "tis", + "tseries", + "xts" + ], + "Imports": [ + "utils", + "graphics", + "grDevices", + "lattice (>= 0.20-27)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://zoo.R-Forge.R-project.org/", + "NeedsCompilation": "yes", + "Author": "Achim Zeileis [aut, cre] (), Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Joshua M. Ulrich [ctb], Felix Andrews [ctb]", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN", + "Encoding": "UTF-8" + } + } +} From feec51a528dcf960e3eef33559839b3d5ffb7bfb Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Thu, 14 Aug 2025 13:31:12 -0400 Subject: [PATCH 02/13] Imputation action files with conda env --- .github/workflows/run_imputation.yml | 123 +++++++++++++++++++++++++++ 1 file changed, 123 insertions(+) create mode 100644 .github/workflows/run_imputation.yml diff --git a/.github/workflows/run_imputation.yml b/.github/workflows/run_imputation.yml new file mode 100644 index 0000000..13131d4 --- /dev/null +++ b/.github/workflows/run_imputation.yml @@ -0,0 +1,123 @@ +name: Imputation Correlation Workflow + +on: + push: + branches: [main] + paths: + - '06_imputation/correlation_workflow.qmd' + pull_request: + branches: [main] + paths: + - '06_imputation/correlation_workflow.qmd' + workflow_dispatch: + +jobs: + r-imputation: + runs-on: ubuntu-22.04 + + env: + RENV_PATHS_ROOT: ~/.local/share/renv # persistent cache location + + steps: + - name: Checkout code + uses: actions/checkout@v4 + + - name: Install pandoc + run: sudo apt-get update && sudo apt-get install -y pandoc + + - name: Set up R + uses: r-lib/actions/setup-r@v2 + + - name: Install system dependencies for R packages + run: | + sudo apt-get update + sudo apt-get install -y build-essential libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev libmagick++-dev libharfbuzz-dev libfribidi-dev libglpk-dev + shell: bash + + - name: Set up Python with conda + uses: conda-incubator/setup-miniconda@v3 + with: + python-version: 3.9 + auto-update-conda: true + + - name: Create and activate conda environment + run: | + conda env remove -n magic_env -y 2>/dev/null || true + conda create -n magic_env python=3.9 -y + source "$(conda info --base)/etc/profile.d/conda.sh" + conda activate magic_env + + # Install compatible packages from conda-forge + conda install -y -c conda-forge numpy=1.24.3 pandas=2.0.3 scipy matplotlib + + # Install MAGIC dependencies + pip install scprep future tasklogger graphtools + + # Clone MAGIC repository + cd 06_imputation + git clone git://github.com/KrishnaswamyLab/MAGIC.git + + # Install MAGIC package + cd MAGIC/python + pip install . + cd ../.. + + # Test MAGIC installation + python -c "import magic; print('MAGIC version:', magic.__version__)" + shell: bash + + - name: Cache R packages (renv) + uses: actions/cache@v4 + with: + path: ${{ env.RENV_PATHS_ROOT }} + key: ${{ runner.os }}-renv-${{ hashFiles('06_imputation/renv.lock') }} + restore-keys: | + ${{ runner.os }}-renv- + + - name: Set repositories + run: Rscript ubuntu.R + + - name: Restore environment from renv.lock + run: | + install.packages("renv", repos = "https://cloud.r-project.org") + renv::restore(prompt = FALSE, lockfile = "06_imputation/renv.lock") + shell: Rscript {0} + + - name: Install R MAGIC package + run: | + source "$(conda info --base)/etc/profile.d/conda.sh" + conda activate magic_env + R --slave << 'EOF' + if (file.exists("06_imputation/renv/activate.R")) { + source("06_imputation/renv/activate.R") + } + install.packages("./06_imputation/MAGIC/Rmagic", repos = NULL, type = "source") + library(Rmagic) + cat("✓ R MAGIC installed and loaded\n") + renv::snapshot() + EOF + shell: bash + + - name: Set up Quarto + uses: quarto-dev/quarto-actions/setup@v2 + + - name: Run imputation correlation workflow + id: render_qmd + run: | + source "$(conda info --base)/etc/profile.d/conda.sh" + conda activate magic_env + cd 06_imputation + quarto render correlation_workflow.qmd + shell: bash + + - name: Deploy HTML to gh-pages + if: success() + run: | + git config --global user.name "github-actions[bot]" + git config --global user.email "github-actions[bot]@users.noreply.github.com" + git fetch origin gh-pages || git checkout --orphan gh-pages + git switch gh-pages || git checkout -b gh-pages + git add 06_imputation/correlation_workflow.html + git commit -m "Deploy correlation_workflow.html [skip ci]" || echo "No changes to commit" + git push origin gh-pages + shell: bash \ No newline at end of file From 250a6fe54f601837051175b0c0242ff97bca0184 Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Mon, 18 Aug 2025 13:14:29 -0400 Subject: [PATCH 03/13] fetch MAGIC package --- .github/workflows/run_imputation.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_imputation.yml b/.github/workflows/run_imputation.yml index 13131d4..989271b 100644 --- a/.github/workflows/run_imputation.yml +++ b/.github/workflows/run_imputation.yml @@ -55,7 +55,7 @@ jobs: # Clone MAGIC repository cd 06_imputation - git clone git://github.com/KrishnaswamyLab/MAGIC.git + git clone https://github.com/KrishnaswamyLab/MAGIC.git # Install MAGIC package cd MAGIC/python From 218b33e15aabb5837afdcd45b164be52d33028f6 Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Tue, 19 Aug 2025 08:58:20 -0400 Subject: [PATCH 04/13] Update run_imputation.yml --- .github/workflows/run_imputation.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_imputation.yml b/.github/workflows/run_imputation.yml index 989271b..e5f2011 100644 --- a/.github/workflows/run_imputation.yml +++ b/.github/workflows/run_imputation.yml @@ -48,7 +48,7 @@ jobs: conda activate magic_env # Install compatible packages from conda-forge - conda install -y -c conda-forge numpy=1.24.3 pandas=2.0.3 scipy matplotlib + conda install -y -c conda-forge numpy=1.24.3 pandas=2.0.3 scipy matplotlib libstdcxx-ng # Install MAGIC dependencies pip install scprep future tasklogger graphtools @@ -120,4 +120,4 @@ jobs: git add 06_imputation/correlation_workflow.html git commit -m "Deploy correlation_workflow.html [skip ci]" || echo "No changes to commit" git push origin gh-pages - shell: bash \ No newline at end of file + shell: bash From 6943adf16a7f1de0c46e4a884602ec60289e4ba9 Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Tue, 19 Aug 2025 10:28:02 -0400 Subject: [PATCH 05/13] Update run_imputation.yml --- .github/workflows/run_imputation.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_imputation.yml b/.github/workflows/run_imputation.yml index e5f2011..dcaba6d 100644 --- a/.github/workflows/run_imputation.yml +++ b/.github/workflows/run_imputation.yml @@ -60,10 +60,15 @@ jobs: # Install MAGIC package cd MAGIC/python pip install . - cd ../.. + # Test MAGIC installation python -c "import magic; print('MAGIC version:', magic.__version__)" + + cd ../Rmagic + R CMD INSTALL . + + cd ../.. shell: bash - name: Cache R packages (renv) @@ -91,7 +96,7 @@ jobs: if (file.exists("06_imputation/renv/activate.R")) { source("06_imputation/renv/activate.R") } - install.packages("./06_imputation/MAGIC/Rmagic", repos = NULL, type = "source") + # install.packages("./06_imputation/MAGIC/Rmagic", repos = NULL, type = "source") library(Rmagic) cat("✓ R MAGIC installed and loaded\n") renv::snapshot() From a4b06027d6c0a3be8ede06f969e1bc52d1a431b7 Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Tue, 19 Aug 2025 11:05:48 -0400 Subject: [PATCH 06/13] adapt the action for Rmagic --- .github/workflows/run_imputation.yml | 30 +++++++++++++++++----------- 1 file changed, 18 insertions(+), 12 deletions(-) diff --git a/.github/workflows/run_imputation.yml b/.github/workflows/run_imputation.yml index dcaba6d..847f3e3 100644 --- a/.github/workflows/run_imputation.yml +++ b/.github/workflows/run_imputation.yml @@ -65,9 +65,6 @@ jobs: # Test MAGIC installation python -c "import magic; print('MAGIC version:', magic.__version__)" - cd ../Rmagic - R CMD INSTALL . - cd ../.. shell: bash @@ -92,11 +89,9 @@ jobs: run: | source "$(conda info --base)/etc/profile.d/conda.sh" conda activate magic_env + cd 06_imputation/MAGIC/Rmagic + R CMD INSTALL . R --slave << 'EOF' - if (file.exists("06_imputation/renv/activate.R")) { - source("06_imputation/renv/activate.R") - } - # install.packages("./06_imputation/MAGIC/Rmagic", repos = NULL, type = "source") library(Rmagic) cat("✓ R MAGIC installed and loaded\n") renv::snapshot() @@ -120,9 +115,20 @@ jobs: run: | git config --global user.name "github-actions[bot]" git config --global user.email "github-actions[bot]@users.noreply.github.com" - git fetch origin gh-pages || git checkout --orphan gh-pages - git switch gh-pages || git checkout -b gh-pages - git add 06_imputation/correlation_workflow.html - git commit -m "Deploy correlation_workflow.html [skip ci]" || echo "No changes to commit" - git push origin gh-pages + OUTPUT_FILE="06_imputation/correlation_workflow.html" + + # Fetch gh-pages (if exists) and create worktree + git fetch origin gh-pages || true + git worktree add /tmp/gh-pages gh-pages 2>/dev/null || git worktree add /tmp/gh-pages -b gh-pages + + # Copy the file into the worktree + mkdir -p "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")" + cp "$OUTPUT_FILE" "/tmp/gh-pages/$(dirname "$OUTPUT_FILE")/" + + cd /tmp/gh-pages + + # Commit and push if there are changes + git add "$(dirname "$OUTPUT_FILE")/$(basename "$OUTPUT_FILE")" + git commit -m "Deploy $(basename "$OUTPUT_FILE") [skip ci]" + git push --force origin gh-pages shell: bash From 1be0c7395ecb0780361951d0181fed8686534328 Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Tue, 19 Aug 2025 11:06:15 -0400 Subject: [PATCH 07/13] update renv --- 06_imputation/renv.lock | 31 ------------------------------- 1 file changed, 31 deletions(-) diff --git a/06_imputation/renv.lock b/06_imputation/renv.lock index a3a5c8f..0a60cbf 100644 --- a/06_imputation/renv.lock +++ b/06_imputation/renv.lock @@ -719,37 +719,6 @@ "Maintainer": "Dirk Eddelbuettel ", "Repository": "CRAN" }, - "Rmagic": { - "Package": "Rmagic", - "Version": "2.0.3.999", - "Source": "unknown", - "Type": "Package", - "Title": "MAGIC - Markov Affinity-Based Graph Imputation of Cells", - "Authors@R": "c(person(given = \"David\", family = \"van Dijk\", role = \"aut\", email = \"davidvandijk@gmail.com\"), person(given = \"Scott\", family = \"Gigante\", role = \"cre\", email = \"scott.gigante@yale.edu\", comment = c(ORCID = \"0000-0002-4544-2764\")))", - "Maintainer": "Scott Gigante ", - "Description": "MAGIC (Markov affinity-based graph imputation of cells) is a method for addressing technical noise in single-cell data, including under-sampling of mRNA molecules, often termed \"dropout\" which can severely obscure important gene-gene relationships. MAGIC shares information across similar cells, via data diffusion, to denoise the cell count matrix and fill in missing transcripts. Read more: van Dijk et al. (2018) .", - "License": "GPL-2 | file LICENSE", - "Depends": [ - "Matrix (>= 1.2-0)", - "R (>= 3.3)" - ], - "Imports": [ - "ggplot2", - "methods", - "reticulate (>= 1.4)", - "stats" - ], - "Suggests": [ - "phateR", - "readr", - "Seurat (>= 3.0.0)", - "viridis" - ], - "Encoding": "UTF-8", - "LazyData": "true", - "RoxygenNote": "7.1.1", - "Author": "David van Dijk [aut], Scott Gigante [cre] (ORCID: )" - }, "Rtsne": { "Package": "Rtsne", "Version": "0.17", From 11bfb29ca204bc908fced6015d11cdf6ccfb8543 Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Thu, 28 Aug 2025 13:40:26 -0400 Subject: [PATCH 08/13] Remove CS-CORE and improve data extraction Removed CS-CORE functionality and updated data extraction methods for Seurat objects. --- 06_imputation/correlation_workflow.qmd | 54 ++++++++++++-------------- 1 file changed, 25 insertions(+), 29 deletions(-) diff --git a/06_imputation/correlation_workflow.qmd b/06_imputation/correlation_workflow.qmd index 89edb7b..2f79d44 100644 --- a/06_imputation/correlation_workflow.qmd +++ b/06_imputation/correlation_workflow.qmd @@ -60,10 +60,8 @@ library(pheatmap) library(gridExtra) library(RColorBrewer) library(viridis) - -library(CSCORE) library(SAVER) -library(Rmagic) +# library(Rmagic) invisible(list2env(params, environment())) source(project_file) @@ -218,30 +216,32 @@ We compare three alternative methods of estimating expression levels to log norm # Store output so we don't have to re-run imputation each time filename <- glue("{path_outs}/imputed.RDS") if (!file.exists(filename)) { - # Get raw counts - raw_rna <- LayerData(seurat, assay = "RNA", layer = "counts") + # Get raw counts (genes x cells matrix) + raw_rna <- as.matrix(GetAssayData(seurat[["RNA"]], slot = "counts")) # SCT # Re-run SCT on subset data seurat <- SCTransform(seurat, return.only.var.genes = FALSE, min_cells = 1) # Creating new seurat object for genes of interest only - data_raw <- FetchData(seurat, assay = "RNA", layer = "counts", vars = corr_genes) - data_rna <- FetchData(seurat, assay = "RNA", layer = "data", vars = corr_genes) - data_sct <- FetchData(seurat, assay = "SCT", layer = "data", vars = corr_genes) + # Use GetAssayData to reliably extract counts/data (features x cells) + data_raw <- as.matrix(GetAssayData(seurat[["RNA"]], slot = "counts")[corr_genes, , drop = FALSE]) + data_rna <- as.matrix(GetAssayData(seurat[["RNA"]], slot = "data")[corr_genes, , drop = FALSE]) + data_sct <- as.matrix(GetAssayData(seurat[["SCT"]], slot = "data")[corr_genes, , drop = FALSE]) seurat_imputed <- CreateSeuratObject( - counts = t(data_raw), - data = t(data_rna), + counts = data_raw, + data = data_rna, meta.data = seurat@meta.data ) - seurat_imputed[["SCT"]] <- CreateAssayObject(data = t(data_sct)) + seurat_imputed[["SCT"]] <- CreateAssayObject(data = data_sct) seurat_imputed[["RAW"]] <- CreateAssayObject(counts = raw_rna) # Delete the original seurat object to save memory rm(seurat) data_magic <- magic(t(raw_rna), genes = corr_genes)$result + # magic returns cells x genes; transpose to features x cells seurat_imputed[["MAGIC"]] <- CreateAssayObject(data = t(data_magic)) # SAVER @@ -293,8 +293,7 @@ We have a few different ways to compute correlation scores with their associated - `SCTransform` counts -> spearman correlation matrix - `MAGIC` imputed -> spearman correlation matrix - `SAVER` imputed -> spearman correlation matrix -2. `CS-CORE` - - Raw RNA counts -> co-expression matrix +2. (removed) `CS-CORE` (this report no longer runs CS-CORE) ```{r correlations} # Store output so we don't have to re-run correlation each time @@ -321,8 +320,15 @@ if (!file.exists(filename)) { gene_2 <- genes_comb[idx, 2] for (assay_ in assays) { - gene_exp <- t(seurat_imputed[[assay_]]$data[c(gene_1, gene_2), ]) %>% - as.data.frame() + # extract assay data safely (features x cells) and subset to the two genes + assay_mat <- tryCatch(as.matrix(GetAssayData(seurat_imputed[[assay_]], slot = "data")), error = function(e) NULL) + if (is.null(assay_mat)) { + gene_exp <- data.frame() + } else { + sub_mat <- assay_mat[c(gene_1, gene_2), , drop = FALSE] + # transpose to cells x genes for cor.test + gene_exp <- as.data.frame(t(sub_mat)) + } if (all(gene_exp[[gene_1]] == 0) | all(gene_exp[[gene_2]] == 0)) { corr_val <- 0.0 @@ -342,15 +348,7 @@ if (!file.exists(filename)) { } } - # Run CS-CORE - DefaultAssay(seurat_imputed) <- "RAW" - CSCORE_result <- CSCORE(seurat_imputed, genes = corr_genes) - - # Store CS-CORE results - tmp <- reshape2::melt(as.matrix(CSCORE_result$est)) %>% rename(CSCORE = value) - df_corr <- left_join(df_corr, tmp) - tmp <- reshape2::melt(as.matrix(CSCORE_result$p_value)) %>% rename(CSCORE = value) - df_p_val <- left_join(df_p_val, tmp) + # CS-CORE removed: no additional co-expression estimates are appended here # Save output write.csv(df_corr, filename) @@ -367,7 +365,7 @@ Showing the patterns of correlation for each method. The x-axis and y-axis are t ```{r visualize-cors} #| fig-width: 7 -methods <- c("RNA", "SCT", "MAGIC", "SAVER", "CSCORE") +methods <- c("RNA", "SCT", "MAGIC", "SAVER") cor_List <- purrr::map(methods, \(method){ corr <- df_corr[c("Var1", "Var2", method)] @@ -381,9 +379,6 @@ cor_List <- purrr::map(methods, \(method){ breaks <- seq(-1, 1, by = 0.1) show_legend <- F - if (method == "CSCORE") { - show_legend <- T - } p <- pheatmap(mtx, color = inferno(10), show_rownames = FALSE, @@ -410,7 +405,7 @@ In these scatterplots, the gene-pairs that are colored red have different result ```{r cor-compare} #| fig-width: 3 #| fig-height: 8 -methods <- c("MAGIC", "SAVER", "CSCORE") +methods <- c("MAGIC", "SAVER") methods_comb <- data.frame(t(combn(methods, 2))) plot_list <- list() @@ -460,3 +455,4 @@ List and version of tools used for the QC report generation. ```{r} sessionInfo() ``` + From 179bd7c8e6f11ab7bcf2c22c58e1ebd8ed2c9c25 Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Thu, 28 Aug 2025 13:52:08 -0400 Subject: [PATCH 09/13] Uncomment Rmagic library import --- 06_imputation/correlation_workflow.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/06_imputation/correlation_workflow.qmd b/06_imputation/correlation_workflow.qmd index 2f79d44..7325b5a 100644 --- a/06_imputation/correlation_workflow.qmd +++ b/06_imputation/correlation_workflow.qmd @@ -61,7 +61,7 @@ library(gridExtra) library(RColorBrewer) library(viridis) library(SAVER) -# library(Rmagic) +library(Rmagic) invisible(list2env(params, environment())) source(project_file) From 5474fd685558c13b7484205abdab1a168aa669af Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Thu, 28 Aug 2025 14:09:24 -0400 Subject: [PATCH 10/13] Refine correlation workflow and update methods Removed references to CS-CORE --- 06_imputation/correlation_workflow.qmd | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/06_imputation/correlation_workflow.qmd b/06_imputation/correlation_workflow.qmd index 7325b5a..a21644e 100644 --- a/06_imputation/correlation_workflow.qmd +++ b/06_imputation/correlation_workflow.qmd @@ -61,7 +61,7 @@ library(gridExtra) library(RColorBrewer) library(viridis) library(SAVER) -library(Rmagic) +# library(Rmagic) invisible(list2env(params, environment())) source(project_file) @@ -106,7 +106,7 @@ min_perc <- 0.2 This report intends to both calculate correlations of gene of interests and also compares how imputation changes those values. -Throughout this report, we assess two main ways of calculating gene correlations scores (**`Spearman` and `CS-CORE`**). +Throughout this report, we assess Spearman correlation estimates. We further assessed two ways of imputating gene expression values: MAGIC and SAVER. @@ -241,8 +241,13 @@ if (!file.exists(filename)) { rm(seurat) data_magic <- magic(t(raw_rna), genes = corr_genes)$result - # magic returns cells x genes; transpose to features x cells - seurat_imputed[["MAGIC"]] <- CreateAssayObject(data = t(data_magic)) + # magic may return a data.frame/tibble or matrix (cells x genes). Force to matrix and transpose to features x cells + if (!is.matrix(data_magic)) data_magic <- as.matrix(data_magic) + data_magic_t <- t(data_magic) + # ensure dimnames align: rows = genes, cols = cells + if (is.null(rownames(data_magic_t))) rownames(data_magic_t) <- corr_genes + if (is.null(colnames(data_magic_t))) colnames(data_magic_t) <- colnames(raw_rna) + seurat_imputed[["MAGIC"]] <- CreateAssayObject(data = data_magic_t) # SAVER # Generate SAVER predictions for those genes @@ -254,6 +259,10 @@ if (!file.exists(filename)) { ncores = parallel::detectCores() - 2 ) + # Ensure SAVER output is a plain matrix with correct dimnames + if (!is.matrix(data_saver)) data_saver <- as.matrix(data_saver) + if (is.null(rownames(data_saver))) rownames(data_saver) <- rownames(raw_rna)[genes.ind] + if (is.null(colnames(data_saver))) colnames(data_saver) <- colnames(raw_rna) seurat_imputed[["SAVER"]] <- CreateAssayObject(data = data_saver) saveRDS(seurat_imputed, filename) @@ -398,7 +407,7 @@ plot(cor_comb) # Compare correlation estimates across methods -Comparing the correlation scores for each gene pair for MAGIC, SAVER, and CS-CORE. +Comparing the correlation scores for each gene pair for MAGIC and SAVER. In these scatterplots, the gene-pairs that are colored red have different results for significance. @@ -442,8 +451,6 @@ grid.arrange(grobs = plot_list, nrow = 3) # Method description -[`CS-CORE`](https://github.com/ChangSuBiostats/CS-CORE) is a R package for cell-type-specific co-expression inference from single cell RNA-sequencing data. It provides an implementation for the statistical method CS-CORE proposed in this [paper](https://www.nature.com/articles/s41467-023-40503-7). - [`MAGIC`](https://github.com/KrishnaswamyLab/MAGIC) is an algorithm for denoising high-dimensional data most commonly applied to single-cell RNA sequencing data. MAGIC learns the manifold data, using the resultant graph to smooth the features and restore the structure of the data. [`SAVER`](https://github.com/mohuangx/SAVER) implements a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data. From 4be5fc19e7c176603ae193f8c6199329ac852f80 Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Thu, 28 Aug 2025 14:09:41 -0400 Subject: [PATCH 11/13] Uncomment Rmagic library in correlation workflow --- 06_imputation/correlation_workflow.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/06_imputation/correlation_workflow.qmd b/06_imputation/correlation_workflow.qmd index a21644e..738e1a9 100644 --- a/06_imputation/correlation_workflow.qmd +++ b/06_imputation/correlation_workflow.qmd @@ -61,7 +61,7 @@ library(gridExtra) library(RColorBrewer) library(viridis) library(SAVER) -# library(Rmagic) +library(Rmagic) invisible(list2env(params, environment())) source(project_file) From f09356a16f580ef7a4b4574852d5a48651f57d45 Mon Sep 17 00:00:00 2001 From: Ruitong Li Date: Thu, 28 Aug 2025 15:29:31 -0400 Subject: [PATCH 12/13] fix the matrix attribute --- 06_imputation/correlation_workflow.qmd | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/06_imputation/correlation_workflow.qmd b/06_imputation/correlation_workflow.qmd index 738e1a9..569e1d7 100644 --- a/06_imputation/correlation_workflow.qmd +++ b/06_imputation/correlation_workflow.qmd @@ -252,17 +252,15 @@ if (!file.exists(filename)) { # SAVER # Generate SAVER predictions for those genes genes.ind <- which(rownames(raw_rna) %in% corr_genes) - data_saver <- saver(raw_rna, + saverD <- raw_rna + attr(saverD, "class") <- "matrix" + data_saver <- saver(saverD, pred.genes = genes.ind, pred.genes.only = TRUE, estimates.only = TRUE, ncores = parallel::detectCores() - 2 ) - # Ensure SAVER output is a plain matrix with correct dimnames - if (!is.matrix(data_saver)) data_saver <- as.matrix(data_saver) - if (is.null(rownames(data_saver))) rownames(data_saver) <- rownames(raw_rna)[genes.ind] - if (is.null(colnames(data_saver))) colnames(data_saver) <- colnames(raw_rna) seurat_imputed[["SAVER"]] <- CreateAssayObject(data = data_saver) saveRDS(seurat_imputed, filename) From 61cbf60fb04639169ef79af0746e98f1c7f63a18 Mon Sep 17 00:00:00 2001 From: Lorena Pantano Date: Fri, 29 Aug 2025 10:33:58 -0400 Subject: [PATCH 13/13] add link in readme --- ...n_imputation.yml => 06_run_imputation.yml} | 0 06_imputation/correlation_workflow.Rmd | 432 ------------------ README.md | 4 + 3 files changed, 4 insertions(+), 432 deletions(-) rename .github/workflows/{run_imputation.yml => 06_run_imputation.yml} (100%) delete mode 100644 06_imputation/correlation_workflow.Rmd diff --git a/.github/workflows/run_imputation.yml b/.github/workflows/06_run_imputation.yml similarity index 100% rename from .github/workflows/run_imputation.yml rename to .github/workflows/06_run_imputation.yml diff --git a/06_imputation/correlation_workflow.Rmd b/06_imputation/correlation_workflow.Rmd deleted file mode 100644 index 37ba431..0000000 --- a/06_imputation/correlation_workflow.Rmd +++ /dev/null @@ -1,432 +0,0 @@ ---- -title: "co-expression with imputation" -author: "Harvard Chan Bioinformatics Core" -date: "`r Sys.Date()`" -output: - html_document: - code_folding: hide - df_print: paged - highlights: pygments - number_sections: true - self_contained: true - theme: default - toc: true - toc_float: - collapsed: true - smooth_scroll: true -params: - project_file: ../information.R - seurat_obj: "https://github.com/bcbio/bcbioR-test-data/raw/refs/heads/main/singlecell/tiny.rds" - group_column: "integrated_snn_res.0.4" - path_outs: "./test_out" - magic_condaEnv: "snapatac2" ---- - -```{r library-load, cache=FALSE, message=FALSE,echo=FALSE} -library(tidyverse) -library(knitr) -library(glue) -library(Seurat) - -library(pheatmap) -library(gridExtra) -library(RColorBrewer) - -library(CSCORE) -library(SAVER) -library(Rmagic) - -invisible(list2env(params, environment())) -source(project_file) -reticulate::use_condaenv(magic_condaEnv, required = T) - -inputRead <- function(f) { - if (sum(endsWith(f, c("rds", "RDS"))) > 0) { - if (R.utils::isUrl(f)) { - f <- url(f) - } - return(readRDS(f)) - } else if (sum(endsWith(f, c("qs", "QS"))) > 0) { - if (R.utils::isUrl(f)) { - f <- url(f) - } - return(qread(f)) - } else { - print("Check file extension and choose appropriate functions!") - } -} -``` - -```{r report-setup,echo=FALSE} -ggplot2::theme_set(theme_light(base_size = 11)) -opts_chunk[["set"]]( - fig.align = "center", - echo = TRUE, - cache = FALSE, - dev = c("png", "pdf"), - error = TRUE, - highlight = TRUE, - message = FALSE, - prompt = FALSE, - tidy = FALSE, - warning = FALSE) -``` - - -```{r filter-parameters} -# Filtration parameters -filter_gene <- FALSE -min_exp <- 0.2 -min_cells <- 40 -min_perc <- 0.2 -``` - -This report intends to both calculate correlations of gene of interests and also compares how imputation changes those values. - -Throughout this report, we assess two main ways of calculating gene correlations scores (**`Spearman` and `CS-CORE`**). - -We further assessed two ways of imputating gene expression values: MAGIC and SAVER. - -More details about the method can be found in the section **Method description**. - -# Overview of project - -- Path seurat: `r seurat_obj` -- Metadata column with cell group label: `r group_column` -- Filter genes based on expression and frequency: `r filter_gene` - -List of all gene of interests: - -```{r gene-of-interests} -corr_genes_all <- c( - "COL1A1", "COL1A2", "DCN", - "EBF2", "IL33", "PRX", "LY6G6C" -) -DT::datatable(data.frame(gene = corr_genes_all)) -``` - -Starting off with `r length(corr_genes_all)` genes of interest. - -# Load seurat object - -```{r seurat-loadin} -seurat <- inputRead(seurat_obj) -Idents(seurat) <- group_column -seurat[["SCT"]] <- NULL -raw_rna <- GetAssayData(object = seurat[["RNA"]], layer = "counts") -genes.use <- rowSums(raw_rna) > 0 -genes.use <- names(genes.use[genes.use]) -seurat <- seurat[genes.use, ] -n_cells <- ncol(seurat) -``` - -From the genes that were supplied, removing any that are not expressed in this dataset. - -```{r only-present} -corr_genes <- corr_genes_all[corr_genes_all %in% genes.use] -``` - -Next we look at the basic distribution of remaining genes of interest in terms of expression and number of cells they are expressed in. - -These are the following filtration metrics that are set: - -- Average expression < `r min_exp` -- Number of cells expressed in > `r min_cells` -- Percentage of cells expressed in > `r min_perc` - -Filtration parameter was set to `r filter_gene`. If FALSE, no further filtration will be done at this step. - -```{r filtered-gene} -data_rna <- FetchData(seurat[["RNA"]], vars = corr_genes) - -# Number of cells a gene is expressed in -num_cells <- colSums(data_rna > 0) -# Percentage of cells a gene is expressed in -perc_cells <- num_cells / ncol(seurat) -# Average expression of a gene -avg_expression <- colMeans(data_rna) - -df_genes <- data.frame(num_cells, perc_cells, avg_expression) -df_genes <- df_genes %>% - mutate(filter = !((perc_cells > min_perc) & - (num_cells > min_cells) & - (avg_expression > min_exp))) -df_genes$gene <- row.names(df_genes) -df_genes <- df_genes %>% arrange(desc(avg_expression), desc(perc_cells)) -df_genes %>% - select(-gene) %>% - magrittr::set_colnames(c( - "N_Cell_Expressed", "Perc_Cell_Expressed", - "Avg_Expression", "Filter" - )) %>% - DT::datatable() %>% - DT::formatRound(columns = c("Perc_Cell_Expressed", "Avg_Expression"), digits = 3) -``` - -```{r visualize-filter,fig.width=6} -df_genes %>% - ggplot(aes(x = perc_cells, y = avg_expression, color = filter)) + - geom_point(size = rel(3)) + - scale_color_manual(values = c("black", "darkred")) + - theme_minimal() + - labs(x = "Percent of cells expressing the gene", y = "Average expression") -``` - -```{r remain-gene} -if (filter_gene == TRUE) { - corr_genes <- (df_genes %>% subset(filter == FALSE))$gene -} -``` - -`r length(corr_genes)` genes of interest remaining. - -# Imputation and normalization - -We compare three alternative methods of estimating expression levels to log normalization and assess their ability to account for dropout. - -1. `SCTransform` (raw counts -> normalized counts) -2. `MAGIC` (raw counts -> imputed, normalized counts) -3. `SAVER` (raw counts -> imputed, normalized counts) - -```{r imputation} -# Store output so we don't have to re-run imputation each time -filename <- glue("{path_outs}/imputed.RDS") -if (!file.exists(filename)) { - # Get raw counts - raw_rna <- LayerData(seurat, assay = "RNA", layer = "counts") - - # SCT - # Re-run SCT on subset data - seurat <- SCTransform(seurat, return.only.var.genes = FALSE, min_cells = 1) - - # Creating new seurat object for genes of interest only - data_raw <- FetchData(seurat, assay = "RNA", layer = "counts", vars = corr_genes) - data_rna <- FetchData(seurat, assay = "RNA", layer = "data", vars = corr_genes) - data_sct <- FetchData(seurat, assay = "SCT", layer = "data", vars = corr_genes) - - seurat_imputed <- CreateSeuratObject( - counts = t(data_raw), - data = t(data_rna), - meta.data = seurat@meta.data - ) - seurat_imputed[["SCT"]] <- CreateAssayObject(data = t(data_sct)) - seurat_imputed[["RAW"]] <- CreateAssayObject(counts = raw_rna) - - # Delete the original seurat object to save memory - rm(seurat) - - data_magic <- magic(t(raw_rna), genes = corr_genes)$result - seurat_imputed[["MAGIC"]] <- CreateAssayObject(data = t(data_magic)) - - # SAVER - # Generate SAVER predictions for those genes - genes.ind <- which(rownames(raw_rna) %in% corr_genes) - data_saver <- saver(raw_rna, - pred.genes = genes.ind, - pred.genes.only = TRUE, - estimates.only = TRUE, - ncores = parallel::detectCores() - 2 - ) - - seurat_imputed[["SAVER"]] <- CreateAssayObject(data = data_saver) - - saveRDS(seurat_imputed, filename) -} - -seurat_imputed <- readRDS(filename) -``` - -## Average expression for each method - -```{r avg-expr,fig.width=6} -assays <- c("RNA", "SCT", "MAGIC", "SAVER") - -df_avg <- data.frame(gene = corr_genes) -for (assay in assays) { - data <- GetAssayData(object = seurat_imputed[[assay]], layer = "data") - avg <- data.frame(rowMeans(data)) - colnames(avg) <- assay - avg$gene <- row.names(avg) - df_avg <- left_join(df_avg, avg, by = "gene") -} - -pheatmap(df_avg %>% column_to_rownames(var = "gene"), - scale = "column", - cluster_col = TRUE, cluster_row = TRUE, - show_rownames = TRUE, - angle_col = 0, color = inferno(10) -) -``` - -# Correlation Estimates - -We have a few different ways to compute correlation scores with their associated p-values: - -1. `Spearman` correlation - - `SCTransform` counts -> spearman correlation matrix - - `MAGIC` imputed -> spearman correlation matrix - - `SAVER` imputed -> spearman correlation matrix -2. `CS-CORE` - - Raw RNA counts -> co-expression matrix - -```{r correlations} -# Store output so we don't have to re-run correlation each time -filename <- glue("{path_outs}/corr.csv") - -if (!file.exists(filename)) { - # Compute spearman correlation for each method (except CS-CORE which is run later) - # Unique combination of each gene pair - genes_comb <- data.frame(t(combn(corr_genes, 2))) - n_comb <- nrow(genes_comb) - - # Create dataframe with correlation and p-values scores - df_corr <- genes_comb %>% rename("Var1" = X1, "Var2" = X2) - df_corr[assays] <- NA - df_p_val <- df_corr - - for (idx in 1:n_comb) { - if (idx %% 200 == 0) { - print(glue("{idx}/{n_comb} correlations computed.")) - } - - # Name of genes to run correlation on - gene_1 <- genes_comb[idx, 1] - gene_2 <- genes_comb[idx, 2] - - for (assay_ in assays) { - gene_exp <- t(seurat_imputed[[assay_]]$data[c(gene_1, gene_2), ]) %>% - as.data.frame() - - if (all(gene_exp[[gene_1]] == 0) | all(gene_exp[[gene_2]] == 0)) { - corr_val <- 0.0 - p_val <- 1.0 - } else { - # Calculate spearman correlation and p-value otherwise - tmp <- cor.test(gene_exp[[gene_1]], gene_exp[[gene_2]], - method = "spearman", exact = FALSE - ) - corr_val <- as.numeric(unname(tmp$estimate)) - p_val <- as.numeric(tmp$p.value) - } - - # Store correlation and p-values - df_corr[idx, assay_] <- corr_val - df_p_val[idx, assay_] <- p_val - } - } - - # Run CS-CORE - DefaultAssay(seurat_imputed) <- "RAW" - CSCORE_result <- CSCORE(seurat_imputed, genes = corr_genes) - - # Store CS-CORE results - tmp <- reshape2::melt(as.matrix(CSCORE_result$est)) %>% rename(CSCORE = value) - df_corr <- left_join(df_corr, tmp) - tmp <- reshape2::melt(as.matrix(CSCORE_result$p_value)) %>% rename(CSCORE = value) - df_p_val <- left_join(df_p_val, tmp) - - # Save output - write.csv(df_corr, filename) - write.csv(df_p_val, glue("{path_outs}/p_corr.csv")) -} - -df_corr <- read.csv(filename, row.names = 1) -df_p_val <- read.csv(glue("{path_outs}/p_corr.csv"), row.names = 1) -``` - -## Heatmap of correlation estimates - -Showing the patterns of correlation for each method. The x-axis and y-axis are the genes of interest with the corresponding correlation value for the pair as the value. Keep in mind that this is symmetric matrix. - -```{r visualize-cors,fig.width=7} -methods <- c("RNA", "SCT", "MAGIC", "SAVER", "CSCORE") - -cor_List <- purrr::map(methods, \(method){ - corr <- df_corr[c("Var1", "Var2", method)] - corr_cp <- corr %>% rename(Var1 = Var2, Var2 = Var1) - corr <- rbind(corr, corr_cp) - mtx <- reshape2::dcast(corr, Var2 ~ Var1) %>% column_to_rownames("Var2") - - # Set the diagonal values: Correlation = 1, p-value = 1 - mtx <- as.matrix(mtx) - diag(mtx) <- 1 - - breaks <- seq(-1, 1, by = 0.1) - show_legend <- F - if (method == "CSCORE") { - show_legend <- T - } - p <- pheatmap(mtx, - color = inferno(10), - show_rownames = FALSE, - show_colnames = FALSE, - breaks = breaks, - main = method, - silent = T, - legend = show_legend, - fontsize = rel(8) - ) - return(p[[4]]) -}) - -cor_comb <- grid.arrange(grobs = cor_List, nrow = 2, ncol = 3) -plot(cor_comb) -``` - -# Compare correlation estimates across methods - -Comparing the correlation scores for each gene pair for MAGIC, SAVER, and CS-CORE. - -In these scatterplots, the gene-pairs that are colored red have different results for significance. - -```{r cor-compare,fig.width=3,fig.height=8} -methods <- c("MAGIC", "SAVER", "CSCORE") -methods_comb <- data.frame(t(combn(methods, 2))) -plot_list <- list() - -for (idx in 1:nrow(methods_comb)) { - method_1 <- methods_comb[idx, 2] - method_2 <- methods_comb[idx, 1] - - corr <- df_corr[c("Var1", "Var2", method_1, method_2)] - p_val <- df_p_val[, c("Var1", "Var2", method_1, method_2)] - corr$sig_1 <- p_val[[method_1]] - corr$sig_2 <- p_val[[method_2]] - - corr <- corr %>% mutate(sig = (sig_1 < 0.5) & (sig_2 < 0.05)) - - p <- ggplot(corr) + - geom_point(aes( - x = get(method_1), y = get(method_2), - color = sig - ), size = rel(3)) + - theme_bw() + - NoLegend() + - scale_color_manual(values = c("FALSE" = "#9D0208", "TRUE" = "black")) + - labs(x = method_1, y = method_2, title = paste(method_1, "vs", method_2)) + - theme(plot.title = element_text(size = rel(1.5))) + - ylim(-1, 1) + - xlim(-1, 1) + - geom_abline(slope = 1, intercept = 0, color = "#63bff0") - - plot_list[[idx]] <- ggplotGrob(p) -} - -grid.arrange(grobs = plot_list, nrow = 3) -``` - -# Method description - -[`CS-CORE`](https://github.com/ChangSuBiostats/CS-CORE) is a R package for cell-type-specific co-expression inference from single cell RNA-sequencing data. It provides an implementation for the statistical method CS-CORE proposed in this [paper](https://www.nature.com/articles/s41467-023-40503-7). - -[`MAGIC`](https://github.com/KrishnaswamyLab/MAGIC) is an algorithm for denoising high-dimensional data most commonly applied to single-cell RNA sequencing data. MAGIC learns the manifold data, using the resultant graph to smooth the features and restore the structure of the data. - -[`SAVER`](https://github.com/mohuangx/SAVER) implements a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data. - -# R session - -List and version of tools used for the QC report generation. - -```{r} -sessionInfo() -``` diff --git a/README.md b/README.md index 47eb9dc..2bc2407 100644 --- a/README.md +++ b/README.md @@ -48,3 +48,7 @@ Read full documentation at [03_differential_expression/README.md](03_differentia # Compositional Analysis ![](https://img.shields.io/badge/status-draft-grey) [`04_compositional/propeller.Rmd`](04_compositional/propeller.Rmd) and [`04_compositional/sscomp.Rmd`](04_compositional/sccomp.Rmd) are templates to run compositional analysis with two different methods. `comp.png` is an example of `sccomp.Rmd` analysis. + +# Gene Expression Imputation + +![](https://img.shields.io/badge/status-stable-green) [`Imputation Analysis`](05_imputation/imputation.qmd) is a template to run gene expression imputation with two different methods, ALRA and MAGIC. 👀 [See an example](https://bcbio.github.io/singlecell-reports/05_imputation/imputation.html) \ No newline at end of file