Immunopeptidogenomics pipeline that builds a cryptic peptide database from RNA-seq and identifies non-canonical (cryptic) peptides in immunopeptidomics mass spectrometry data.

Modular RNA-seq variant calling and annotation framework (hg38) integrating STAR and GATK Best Practices to extract high-confidence SNPs and enable gene-level and systems biology analyses of expressed genetic variation.

ORACLE RNA-seq pipeline — STAR + DESeq2 + GSEA, multi-species, metadata-driven design

Differential gene expression analysis for samples with replicates using STAR-DeSeq2 pipeline

Automated RNA-seq reference builder for STAR and Salmon. Features container-aware memory detection, automatic Ensembl/GENCODE downloads, and version-controlled index generation.

RNA-Sequencing

Bulk RNA-seq pipeline: transcriptional characterization of anti-PD1 responders vs non-responders in metastatic melanoma

Containerized, end-to-end RNA-seq differential expression pipeline. FASTQ → DEGs → pathway enrichment in one command. Powered by STAR, DESeq2, and Snakemake. Runs on Windows and Linux via Docker.

End-to-end RNA-seq pipeline for BRCA tumor vs normal differential expression analysis

End-to-end RNA-seq differential expression analysis workflow for RUNX3 knockout gastric cancer cells using STAR, MultiQC, featureCounts and DESeq2.

Workflow for differential gene expression analysis for non-replicate samples using DEGseq

Reproducible RNA-seq workflow using STAR, featureCounts, and OOP Python deployed on AWS

counting Insertion (I), deletion (D), splcing(N) events from CIGAR string in sam file generated by STAR aligner

A modular, containerized NGS pipeline for RNA-seq, long-read, and metagenomic analysis