Popular repositories Loading

1. cutandrun-pipeline cutandrun-pipeline Public

   A modular, production-ready Snakemake pipeline for CUT&RUN epigenomic analysis — featuring E. coli spike-in normalization, SEACR peak calling, fragment size analysis, and comprehensive QC reporting…

   Python

2. chipseq-pipeline chipseq-pipeline Public

   A production-ready, modular Snakemake pipeline for end-to-end ChIP-seq analysis. Features include robust sample-sheet validation, automated QC gating, background-aware peak calling (MACS2), and con…

   Python

3. atacseq-pipeline atacseq-pipeline Public

   A production-grade, modular Snakemake pipeline for reproducible ATAC-seq analysis, featuring upfront configuration validation and robust QC gating.

   Python

4. .github .github Public

5. RNAseq-pipeline RNAseq-pipeline Public

   Production-grade, modular Snakemake pipeline for RNA-seq analysis. Includes QC (FastQC, fastp), alignment (STAR), quantification (featureCounts), post-alignment QC (RSeQC, Preseq, Picard), DESeq2 …

   Python

6. AlphaGenomeR AlphaGenomeR Public

   R interface to Google DeepMind AlphaGenome API. Bridging gRPC-based multimodal genomic predictions (RNA-seq, ATAC, Splicing, 3D Genome) into R-native workflows.

   R