ChIP-seq analysis: QC and contamination screening, Bowtie2 alignment, MACS2 broad peaks, DiffBind, and monaLisa/JASPAR motif enrichment, with a MultiQC report.

Reproducible ChIP-seq analysis pipeline for GSE107221 using Galaxy, ChIPseeker and DiffBind to identify KDM5A-regulated H3K4me3 loci.

Comparative ATAC-seq analysis of Alzheimer's Disease and Medulloblastoma microglia using BWA, SAMtools, MACS2, DiffBind, BEDTools, and HOMER to identify shared chromatin accessibility patterns.

Self-hosted CUT&RUN bioinformatics platform for the Ferguson Lab at UCSD. Replicates CUTANA Cloud and extends it with trimming, SEACR/MACS2, DiffBind, custom heatmaps, Pearson correlation, & Roman normalization. React + FastAPI + PostgreSQL on EC2.