oldpackages.csv

# List of Scientific software developed by the P01
#
# The 'repo' column only needs to be added if the repository is located in a
# place other than the USCBiostats GitHub organization.
#
# The 'on_bioc' column only needs to be specified with 'TRUE' if the package
# is in BioConductor.
#
# The 'google_scholar' column can be included if the package has a link to
# citations in Google scholar, the 'Cited by' section.
#
name,repo,on_bioc,google_scholar,description
"aphylo",,,"https://scholar.google.com/scholar?oi=bibs&hl=en&cites=31698742435768054,3381716696595820644&as_sdt=5","Statistical inference of genetic functions in phylogenetic trees"
"bayesnetworks",,,,"C++ program to fit Bayesian networks, illustrated with simulated data"
"BinaryDosage",,,,"Converts VCF files to a binary format"
"causnet",,,,"Finds a globally optimal causal network given some data as input."
"fdrci",,,"https://scholar.google.com/scholar?hl=en&cites=6606625444967735035","Permutation-Based FDR Point and Confidence Interval Estimation"
"fmcmc",,,"https://scholar.google.com/scholar?cites=18235425292318567621&hl=en","A friendly MCMC framework"
"GxEScanR",,,,"R version of GxEScan"
"HiLDA",,"TRUE","https://scholar.google.com/scholar?cites=2767354745053140554&hl=en","An R package for inferring the mutational exposures difference between groups"
"iMutSig",,,"https://scholar.google.com/scholar?cites=16599818872657505515&hl=en","A web application to identify the most similar mutational signature using shiny"
"jsPhyloSVG",,,,"htmlwidgets for the jsPhyloSVG JavaScript library"
"LUCIDus",,,"https://scholar.google.com/scholar?cites=17993227897179669521&hl=en","Latent and Unknown Cluster Analysis using Integrated Data"
"MergeBinaryDosage",,,,"R package for merging binary dosage files"
"rphyloxml",,,,"Read and write phyloXML files in R"
"selectKSigs",,"TRUE",,"Selection of K in finding the number of mutational signatures"
"slurmR",,,"https://scholar.google.com/scholar?cites=2044081763350723149&hl=en","slurmR: A Lightweight Wrapper for Slurm"
"partition",,,"https://scholar.google.com/scholar?cites=5586649186160622454&hl=en","A fast and flexible framework for agglomerative partitioning in R "
"polygons",,,,"Flexible functions for computing polygons coordinates in R "
"xtune",,,"https://scholar.google.com/scholar?cites=12002990865154112222&hl=en","An R package for Lasso and Ridge Regression with differential penalization based on prior knowledge "
"xrnet",,,"https://scholar.google.com/scholar?cites=12362903479655163477&hl=en","R Package for Hierarchical Regularized Regression to Incorporate External Data"
"hJAM",,,"https://scholar.google.com/scholar?cites=5_2ea7Z8nBIJ&hl=en","hJAM is a hierarchical model which unifies the framework of Mendelian Randomization and Transcriptome-wide association studies."
"AnnoQR",,,,"R client wrap for AnnoQ API (https://github.com/blueOwl/AnnoQR)"
"pfamscanr",,,,"An R client for EMBL-EBI's PfamScan API"
"methcon5",https://github.com/USCbiostats/MethCon5,,"https://scholar.google.com/scholar?cites=13818868965517630908&hl=en","R package to identify and rank CpG DNA methylation conservation along the human genome"
"cit",,,"https://scholar.google.com/scholar?cites=2897292192206854993&hl=en","Causal Inference Test"
"gesso",,,"https://scholar.google.com/scholar?cites=PbkWjCSETP0J&hl=en","Hierarchical GxE Interactions in a Regularized Regression Model"