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…
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.
Genomic annotation of ChIP-seq/ATAC-seq peaks, showing where in the genome your signal actually lands.
This is a repository to show my experience analyzing different kinds of Omics data.
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)
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!
Bulk ATAC-seq Snakemake workflow: Compatible with local and LSF-based HPC systems
ATAC-seq chromatin accessibility pipeline with MACS2 peak calling
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