FlowPath Dynamics is a professional, publication-ready R Shiny application designed for automated flow cytometry dose-response profiling. It supports both specialized Annexin V/PI Apoptosis Assays and Multi-Channel Phenotypic Analysis, providing high-throughput quantification from raw FCS files to statistical inference.
No installation required. Access the full suite directly at:
https://huggingface.co/spaces/mahmood-iab/FACS-Analysis
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Dual Analysis Engines: Switch between specialized Apoptosis profiling and a new, combinatorial Multi-Channel Generic mode (up to
$2^N$ populations). - Absolute Quantification: Integrated volumetric cell counting using counting beads (e.g., Precision Count Beads™).
- Control Viability Guard: Automated alerts for "failed experiments" (Control Viability < 70%) to prevent misleading normalization.
- Improved Compensation Engine: High-performance spillover calculation using top-percentile peak detection and ArcSinh transformation for expanded "cloud" visualization.
- Dynamic Analysis Engine: Instant results recalculation (curves, stats, plots) without re-processing raw files.
- Interactive Data Exclusion: Real-time replicate exclusion with visual feedback and outlier detection (Grubbs Test).
- Advanced Statistics: Statistical inference using One-Way ANOVA on Log10-potency values with Tukey HSD post-hoc testing and automated hypothesis interpretation.
- Publication Graphics: Automatic generation of Therapeutic Window plots, violin plots (MFI), and high-resolution reports.
Files must follow this standardized format for automatic metadata extraction:
CellLine_Treatment_ConcentrationuM_Replicate.fcs
Examples:
Ly1_CompoundX_10uM_Rep1.fcsNUDUL1_DMSO_0uM_Rep3.fcs(Control)
- Upload: Add batch FCS files and optional single-stained controls.
- Setup: Select your analysis mode (Apoptosis vs. Generic) and enable Absolute Counting if beads were used.
- Compensate: Calculate or manually fine-tune the spillover matrix.
- Gate: Interactive hierarchical gating (Beads → FSC/SSC → Singlets → Marker Thresholds).
- Review: Verify gates across all cell lines in the visual dashboard.
- Analyze: Run the engine to fit curves and perform pairwise statistical comparisons.
- Export: Download a comprehensive ZIP package including a 20+ page technical HTML report.
Powered by the drc package, the app iteratively attempts:
- LL.4: Four-parameter log-logistic (Standard).
- LL.3: Three-parameter (Fixed upper limit).
- Weibull (W1.4/W2.4): Robust alternatives for non-standard responses.
- IC50/LD50/EC50: Half-maximal effective concentrations with 95% CI.
- Therapeutic Window: Distance-based comparison of potency vs. toxicity.
- Absolute Survival: Normalization to bead-based volumetric concentration to capture total cell loss.
- Technical Report: Comprehensive HTML documentation of methodology, gating, and results.
- Data Tables: CSV files for Raw Quadrant Data, IC50/EC50 Results, QC Metrics (CV%), and Tukey HSD Stats.
- High-Res Figures: 300 DPI PNG/SVG exports of all generated plots.
- Traceability: Exported compensation matrices and gate coordinates.
Run locally in RStudio using the following dependencies:
# Bioconductor
BiocManager::install("flowCore")
# CRAN
install.packages(c("shiny", "bslib", "ggplot2", "dplyr", "tidyr", "readr",
"stringr", "drc", "scales", "sp", "zip", "svglite",
"outliers", "DescTools", "gridExtra", "rmarkdown",
"kableExtra", "DT", "ggrepel", "knitr", "htmltools"))Mahmood Mohammed Ali | Version 3.1 Université Grenoble Alpes | Institute for Advanced Biosciences (IAB) Epigenetics of Regeneration and Cancer Group mahmood.mohammed-ali@univ-grenoble-alpes.fr
Software DOI: Mahmood MOHAMMED ALI. (2025). Mahmood-M-Ali/FlowIC50: v3.1 (v3.1). Zenodo. https://doi.org/10.5281/zenodo.17872796