A course on genomics and bioinformatics from WashU
Differential accessibility, LRT tests and timecourse analyses for chromatin accessibility data
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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.
This is an automated workflow pipeline for analyzing bulk ATAC-seq data, implemented primarily in bash scripts, and wrapped in a NextFlow workflow.
This repository consists of two **Jupyter Notebooks** created to document a comparison of a mouse brain snATAC-seq (single nuclei assay for transposase accessible chromatin with sequencing) data set from http://catlas.org/mousebrain/ with a scRNA-seq (single cell RNA sequencing) data set from the Linnarsson lab's http://mousebrain.org/. Specific…
Genomic annotation of ChIP-seq/ATAC-seq peaks, showing where in the genome your signal actually lands.
The project focuses on the devlopment and refinement of a Machine Learning model enabling the prediction of chromatin accessibility variation at the genomic window level (of size 1Mbp or 0.1Mbp)
Execution-capable genomics workflow agent for reproducible NGS QC, variant-QC, nf-core orchestration, provenance, and agentic reporting.
TSS enrichment metagene profile, the key quality signal for ATAC-seq and ChIP-seq experiments.
Yet another ATACseq pipeline written in Nextflow, but this one is different (so said everyone). See the DAG, if you prefer the components in this pipeline, give it a spin!
This is a repository to show my experience analyzing different kinds of Omics data.
ATAC-seq chromatin accessibility pipeline with MACS2 peak calling
Bulk ATAC-seq Snakemake workflow: Compatible with local and LSF-based HPC systems
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