star-aligner

RNA-seq analysis from FASTQ to biology: STAR alignment, gene-level counts, DESeq2 differential expression, and GO/KEGG/GSEA. Metadata-driven design with human/mouse/rat support.

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

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

Empirical benchmark suite comparing execution times, peak RAM usage, and cloud compute costs across RNA-Seq aligners, single-cell frameworks, and variant callers.

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.

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

Parallel end-to-end bulk RNA-seq pipeline on a PBS/HPC job array: FastQC, Trimmomatic, STAR alignment, and featureCounts, with a Bioconda setup script.

RNA-Sequencing

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

RNA-seq QC benchmark (custom Python vs FastQC), adapter trimming, STAR alignment, and htseq-count-based strand-specificity analysis

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

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

Independently maintained, performance-oriented successor to the STAR RNA-seq aligner

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

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

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

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

STAR + featureCounts + DESeq2 bulk RNA-seq as a Snakemake DAG, with SLURM/AWS profiles, SQLite, PySpark, and a verified Airflow DAG