ChIP-seq analysis notes from Ming Tang
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Aug 5, 2024 - Python
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chip-seq
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MACS -- Model-based Analysis of ChIP-Seq
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Nov 27, 2025 - Python
A collection of Galaxy-related training material
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Jan 13, 2026 - HTML
🎯 ChIP peak Annotation, Comparison and Visualization
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Nov 4, 2025 - R
ChIP-seq peak-calling, QC and differential analysis pipeline.
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Nov 21, 2025 - Nextflow
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
bioinformatics rna-seq snakemake pipeline reproducible-research ngs bioinformatics-pipeline chip-seq atac-seq workflows fastq sra
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Nov 22, 2025 - Python
Publication quality NGS track plotting
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Oct 10, 2025 - Python
AQUAS TF and histone ChIP-seq pipeline
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Jun 21, 2022 - Java
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
bioinformatics dnase-seq genomics ngs motif chip-seq atac-seq motif-analysis footprinting differential-peak-calling
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Nov 3, 2025 - Python
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
workflow rna-seq pipeline nextflow shiny deseq2 microarray chip-seq atac-seq differential-expression limma gsea nf-core differential-abundance
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Jan 9, 2026 - Nextflow
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.
visualization workflow bioinformatics gene-sets rna-seq snakemake pipeline chip-seq atac-seq gene-set-enrichment enrichment-analysis genomic-regions biomedical-data-science motif-enrichment-analysis
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Sep 24, 2025 - Python
A Snakemake workflow and MrBiomics module for performing and visualizing differential analyses of NGS data powered by the R package limma.
visualization workflow bioinformatics rna-seq snakemake r statistics dea scrna-seq chip-seq atac-seq limma biomedical-data-science differential-expression-analysis volcano-plot limma-voom limma-trend
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Nov 25, 2025 - R
A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.
visualization workflow bioinformatics rna-seq snakemake integration pipeline ngs dimensionality-reduction chip-seq atac-seq normalization biomedical-data-science batch-effect count-matrix confounding-effects
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Jan 9, 2026 - R
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
tfs roadmap gene rna-seq motif gene-expression regulation epigenetics encode cell chip-seq hotspot plasticity transcription-factor-binding motifs epigenomics fimo haystack-bio specific-regions haystack-pipeline
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Jun 21, 2022 - HTML
Go / Golang Bioinformatics Library
golang coverage bam-files bioinformatics bigwig chip-seq golang-library gtf bigwig-files bioinformatics-containers genomic-ranges
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Oct 13, 2024 - Go
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