RNA-seq Differential Expression Analysis Pipeline v1.0.0 This is the first official release of the RNA-seq differential expression analysis pipeline for HiPerGator. This version has been validated and is suitable for citation in publications but will continue to be rapidly updated to improve ease of us and documentation and to align its configuration with other UFHCC-BCBSR tools. Key Features Analysis Methods Multiple DE tools: DESeq2, edgeR GLM, and limma-voom Flexible gene filtering: edgeR filterByExpr and NOISeq filtered.data TMM normalization with batch effect correction support Automated GO enrichment analysis Interactive Shiny Application User-friendly parameter configuration and job submission interface Sample and contrast file validation Real-time preview of analysis parameters Automated report generation Comprehensive Reporting Reproducible analysis reports with full method descriptions Publication-ready visualizations (PCA, heatmaps, volcano plots, MA plots) Gene-level statistics and enrichment results Export of filtered count matrices and differential expression tables HiPerGator Integration Optimized for UF HiPerGator HPC environment Parallel processing support RSEM count matrix input compatibility (upcoming: start from raw counts matrix) Citation Users citing this pipeline should reference: UFHCC-BCBSR/app-rnareportR v1.0.0 Notes This release represents a stable, production-ready version Active development continues with additional features planned For issues or feature requests, please use the GitHub issue tracker System Requirements R >= 4.0 Required packages: edgeR, DESeq2, limma, NOISeq, clusterProfiler, shiny Designed for HiPerGator but portable to other HPC systems