deepStats: a stastitical toolbox for deeptools and genomic signals
ChIP-seq analysis: QC and contamination screening, Bowtie2 alignment, MACS2 broad peaks, DiffBind, and monaLisa/JASPAR motif enrichment, with a MultiQC report.
Reproducible Snakemake workflow for spike-in–normalized ATAC-seq — concatenated-genome alignment, MACS2 peaks, a consensus fragment-count matrix, an interactive QC report, and DESeq2 differential binding. Docker/Apptainer-ready.
End-to-end Snakemake ATAC-seq pipeline (spike-in-free): Bowtie2 → MACS2 → reproducible fixed-width consensus peaks + a self-contained interactive QC report, plus opt-in CTCF-anchored differential openness (DESeq2) and TF footprinting (TOBIAS). Fully containerized (Docker/Apptainer).
Reproducible Snakemake ChIP-seq pipeline: Bowtie2 → MACS2 (narrow/broad, input/IgG control) → IDR & consensus peaks → ENCODE-grade QC → differential binding, peak annotation & motif enrichment. Containerized (Docker/Apptainer)
Reproducible Snakemake workflow for paired-end CUT&RUN (no spike-in): MACS2 + SEACR peak calling with matched IgG/Input controls, mode-aware consensus count matrices, ENCODE-grade QC, and opt-in DESeq2 differential binding + ChIPseeker/HOMER downstream analysis
An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.
Workshops, Course Schedule and Teaching Assistant Review from my time as a chosen Undergraduate Teaching Assistant for the University of Pittsburgh course, BIOSC1540 - Computational Genomics taught by Dr. Miler Lee.
Independent project I undertook to perform a full ChIP-Seq analysis of the transcription factor Nanog in Zebrafish embryos.
DNA methylation analysis pipeline using Bismark and deepTools
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