Pinned Loading

1. rna-seq-pipeline rna-seq-pipeline Public

   A reproducible RNA-seq analysis pipeline built with Nextflow and Docker, supporting QC, alignment, quantification, differential expression, transcript discovery, and automated reporting.

   Nextflow

2. gsea-analysis gsea-analysis Public

   Reproducible Nextflow DSL2 pipeline for gene set enrichment analysis using DESeq2, fgsea, Docker, and publication-quality visualization.

   Nextflow

3. rare-disease-foundation-model-benchmark rare-disease-foundation-model-benchmark Public

   Benchmarking DNA and protein foundation models for rare disease variant interpretation.

4. regulatory-multiomics-pipeline regulatory-multiomics-pipeline Public

   Reproducible Nextflow workflow integrating bulk RNA-seq, ATAC-seq, WGBS, and H3K27ac ChIP-seq for regulatory multi-omics analysis with provenance and external validation.

   Python

5. wgs-pipeline wgs-pipeline Public

   Reproducible Nextflow DSL2 pipeline for short-read human WGS, supporting germline and matched tumor-normal variant calling, benchmarking, SV/CNV analysis, QC, reporting, and provenance.

   Python

6. hypothetical-proteins-amr hypothetical-proteins-amr Public

   Investigating hypothetical proteins and their potential roles in antimicrobial resistance.