An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.
A Snakemake workflow and MrBiomics module for performing and visualizing differential expression analyses (DEA) on NGS data powered by the R package limma.
A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from experiments with sequencing readout (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including diagnostic visualizations.
CWL based Bioinformatics Workflows
Computational biology/bioinformatics workflows, codes, and concept notes on NGS data
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
Multiple-replica multiple-condition Macs2 ChIPSeq wrapper
ChIP-Seq processing pipeline on snakemake
MACS -- Model-based Analysis of ChIP-Seq
WDL workflow language program, developed for singlecell rna sequencing data analysis, maintained by @OOAAHH(SunHao) .
🎯 ChIP peak Annotation, Comparison and Visualization
Improving the feature density based peak caller with dynamic statistics
Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
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