“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. ”

169

GitPedia Card896/001

COMMON

⭐133HP

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🔮Psychic

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pyflow-ChIPseq

crazyhottommy

Pythonchip-seqpython

“a snakemake pipeline to process ChIP-seq files from GEO or in-house ”

SparK

harbourlab

Pythonbedgraph-fileschip-seq

“Publication quality NGS track plotting”

reg-gen

CostaLab

Pythonatac-seqbioinformatics

“Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.”

chipseq_pipeline

kundajelab

Javachip-seqchip-seq-pipelines

“AQUAS TF and histone ChIP-seq pipeline”

differentialabundance

nf-core

Nextflowatac-seqchip-seq

“Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq ”

enrichment_analysis

epigen

Pythonatac-seqbioinformatics

“A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.”

dea_limma

epigen

Ratac-seqbioinformatics

“A Snakemake workflow and MrBiomics module for performing and visualizing differential analyses of NGS data powered by the R package limma.”

spilterlize_integrate

epigen

Ratac-seqbatch-effect

“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.”