Projects in Awesome Lists tagged with chip-seq

https://github.com/crazyhottommy/chip-seq-analysis

ChIP-seq analysis notes from Ming Tang

chip-seq histone-modifications transcription-factor-binding

Last synced: 16 May 2025

https://github.com/crazyhottommy/ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang

chip-seq histone-modifications transcription-factor-binding

Last synced: 19 Apr 2025

https://github.com/deeptools/deepTools

Tools to process and analyze deep sequencing data.

bioinformatics chip-seq genomics ngs python rna-seq

Last synced: 19 Apr 2025

https://github.com/macs3-project/MACS

MACS -- Model-based Analysis of ChIP-Seq

atac-seq chip-seq dnase-seq macs peak-caller poisson-equation python

Last synced: 19 Apr 2025

https://github.com/maxplanck-ie/snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data

atac-seq bisulfite-sequencing chip-seq hi-c ngs rna-seq snakemake workflow

Last synced: 17 Mar 2026

https://github.com/galaxyproject/training-material

A collection of Galaxy-related training material

chip-seq hacktoberfest materials metagenomics ngs proteomics rnaseq training tutorial usegalaxy

Last synced: 15 May 2025

https://github.com/nf-core/chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

chip chip-seq chromatin-immunoprecipitation macs2 nextflow nf-core peak-calling pipeline workflow

Last synced: 16 Jan 2026

https://github.com/vanheeringen-lab/seq2science

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.

atac-seq bioinformatics bioinformatics-pipeline chip-seq fastq ngs pipeline reproducible-research rna-seq snakemake sra workflows

Last synced: 21 Aug 2025

https://github.com/kundajelab/chipseq_pipeline

AQUAS TF and histone ChIP-seq pipeline

chip-seq chip-seq-pipelines genomics

Last synced: 27 Jan 2026

https://github.com/crazyhottommy/pyflow-chipseq

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

chip-seq python snakemake

Last synced: 06 May 2025

https://github.com/dputhier/pygtftk

A python package and a set of shell commands to handle GTF files

bed bigwig bioinformatics cds chip-seq dna-sequences exon gene genomic genomics gtf intron ngs rna-seq splicing transcript tss tts

Last synced: 14 Jan 2026

https://github.com/pinellolab/haystack_bio

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

cell chip-seq encode epigenetics epigenomics fimo gene gene-expression haystack-bio haystack-pipeline hotspot motif motifs plasticity regulation rna-seq roadmap specific-regions tfs transcription-factor-binding

Last synced: 06 Feb 2026

https://github.com/pbenner/gonetics

Go / Golang Bioinformatics Library

bam-files bigwig bigwig-files bioinformatics bioinformatics-containers chip-seq coverage genomic-ranges golang golang-library gtf

Last synced: 16 Mar 2025

https://github.com/epigen/enrichment_analysis

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

atac-seq bioinformatics biomedical-data-science chip-seq enrichment-analysis gene-set-enrichment gene-sets genomic-regions motif-enrichment-analysis pipeline rna-seq snakemake visualization workflow

Last synced: 15 Apr 2025

https://github.com/tushiqi/manorm2

MAnorm2 for Normalizing and Comparing ChIP-seq Samples

chip-seq differential-analysis empirical-bayes r-package winsorize-values

Last synced: 20 Feb 2026

https://github.com/jetbrains-research/bioinf-commons

Bioinformatics library in Kotlin

2bit bam bed bioinformatics cancellable chip-seq dataframe dataset dna-sequence fasta fastq hmm hypothesis-testing kotlin methylation mixture progress sampling

Last synced: 19 Oct 2025

https://github.com/epigen/dea_limma

A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.

atac-seq bioinformatics biomedical-data-science chip-seq differential-expression-analysis limma limma-trend limma-voom r rna-seq scrna-seq snakemake statistics visualization volcano-plot workflow

Last synced: 15 Apr 2025

https://github.com/epigen/open_pipelines

Pipelines for NGS data preprocessing by the Bock lab and friends

atac-seq bioinformatics chip-seq looper ngs-pipeline pipeline pypiper rna-seq

Last synced: 11 Aug 2025

https://github.com/genometric/mspc

Using combined evidence from replicates to evaluate ChIP-seq peaks

analysis chip-seq enriched-regions genome-analysis mspc next-generation-sequencing ngs-analysis overlapping-peaks peak peaks

Last synced: 12 Apr 2025

https://github.com/epigen/spilterlize_integrate

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.

atac-seq batch-effect bioinformatics biomedical-data-science chip-seq confounding-effects count-matrix dimensionality-reduction integration ngs normalization pipeline rna-seq snakemake visualization workflow

Last synced: 24 Aug 2025

https://github.com/guigolab/chip-nf

An automated ChIP-seq pipeline using Nextfow

chip-seq crg guigo guigolab-nf nextflow ngs pipeline

Last synced: 14 Jan 2026

https://github.com/robertamezquita/marge

API for HOMER in R for Genomic Analysis using Tidy Conventions

bioinformatics chip-seq r

Last synced: 28 Apr 2025

https://github.com/darwinawardwinner/cd4-csaw

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

bioconductor bioinformatics-pipeline chip-seq r reproducible-research rna-seq

Last synced: 23 Apr 2025

https://github.com/afrendeiro/toolkit

A toolkit for NGS analysis with Python

atac-seq bioinformatics chip-seq looper ngs ngs-analysis project-management pypiper rna-seq

Last synced: 05 Oct 2025

https://github.com/soedinglab/bammmotif2

Bayesian Markov Model motif discovery tool version 2 - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.

bioinformatics chip-seq motif-analysis motif-discovery ngs-analysis

Last synced: 27 Apr 2025

https://github.com/ibn-salem/sevenc

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

3d-genome chip-seq chromatin-interaction hi-c prediction r-package sequence-motif transcription-factors

Last synced: 18 Feb 2026

https://github.com/soedinglab/peng-motif

PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.

bioinformatics chip-seq dna motif-discovery rna

Last synced: 27 Apr 2025

https://github.com/jetbrains-research/span

SPAN Peak Analyzer

bioinformatics chip-seq peak-caller

Last synced: 18 Jul 2025

https://github.com/ay-lab/chipline

ChIP-seq analysis pipeline

chip-seq idr macs2 qc

Last synced: 26 Dec 2025

https://github.com/saketkc/moca

:m: Tool for motif conservation analysis

bioinformatics chip-seq motif-discovery transcription-factor-binding transcription-factors

Last synced: 12 Apr 2025

https://github.com/showteeth/debpeak

DEbPeak - Analyze and integrate multi-omics to unravel the regulation of gene expression.

analysis atac-seq chip-seq count-matrix differential-expression geo integration m6a-seq peak-related rna-seq transcription-factors visualization

Last synced: 01 Apr 2026

https://github.com/j-andrews7/onelineromics

One liner analyses and visualizations for bulk RNA-seq and ChIP-seq data

chip-seq genomics genomics-visualization oneliner-commands oneliners pipelines r rna-seq visualizations

Last synced: 24 Jun 2025

https://github.com/adeschen/similarpeak

Bioconductor Package - Metrics to estimate the level of similarity between two ChIP-Seq profiles

bioconductor bioconductor-package chip-profiles chip-seq metrics r

Last synced: 18 Mar 2025

https://github.com/ltla/csawusersguide

Clone of the Bioconductor repository for the csawUsersGuide workflow.

bioconductor chip-seq r

Last synced: 10 Apr 2025

https://github.com/olegs/bioinformatics

Reviews on NGS data analysis methods

atac-seq chip-seq differential-chip-seq

Last synced: 26 Jun 2025

https://github.com/mbelmadani/motifgp

Motif discovery for DNA sequences using multiobjective optimization and genetic programming.

bioinformatics chip-seq deap dna dna-sequences genetic-programming jaspar motif motif-discovery multiobjective-optimization network-expressions nsga-ii pareto-front python regular-expressions sequences strongly-typed transcription-factor-binding transcription-factors

Last synced: 07 Jul 2025

https://github.com/poisonalien/chiptk

optimized protocol for processing 50-bp SE ChIP-seq

chip-seq pipeline-runner super-enhancers

Last synced: 14 Oct 2025

https://github.com/mahshaaban/target

target: An R Package to Predict Combined Function of Transcription Factors

algorithm chip-seq dna-binding gene-regulation r-package transcription-factors

Last synced: 18 Feb 2026

https://github.com/sjessa/chromswitch

An R/Bioconductor package for detecting chromatin state switches

bioconductor bioinformatics chip-seq epigenomics r

Last synced: 18 Feb 2026

https://github.com/jetbrains-research/chipseq-smk-pipeline

ChIP-Seq processing pipeline on snakemake

atac-seq chip-seq peak-calling pipeline quality-control snakemake visualization

Last synced: 09 Jul 2025

https://github.com/ltla/csaw

Clone of the Bioconductor repository for the csaw package.

bioconductor-package chip-seq

Last synced: 27 Jul 2025

https://github.com/mahshaaban/integratingdatabioc

Source code for the Bioconductor workshop "Integrating gene expression and DNA-binding data using R/Bioconductor"

bioconductor-packages chip-seq gene-expression rna-se transcription-factors

Last synced: 19 Feb 2026

https://github.com/j-andrews7/eclipse

An R package for classifying, comparing, and investigating sub-region structural changes of (super) enhancers (or other large domains).

bioconductor chip-seq classification cutandrun epigenetics regulation super-enhancers

Last synced: 20 Sep 2025

https://github.com/neurogenomics/motifpeeker

Benchmark Epigenomic Profiling Methods with Motif Enrichment as Key Metric

bioconductor bioconductor-package chip-seq epigenomics interactive-report motif-enrichment-analysis r-package

Last synced: 03 Apr 2025

https://github.com/humburg/chipsim

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/ChIPsim.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=ChIPsim.

bioconductor-packages chip-seq simulation

Last synced: 08 Apr 2025

https://github.com/stevekm/peak-type-summary

ChIPSeeker genomic region summary plotting and annotation script

chip-seq peaks plot reporting

Last synced: 29 Oct 2025

https://github.com/crazyhottommy/epigenome_roadtrip

my RoadTrip project

chip-seq chromatin-state machine-learning

Last synced: 24 Jul 2025

https://github.com/lanl/slur-m-py

SLUR(M)-py (pronounced slurpy): A SLURM Powered Pythonic Pipeline for Parallel Processing of 3D (Epi)genomic Profiles

atac-seq chip-seq hi-c slurm

Last synced: 29 Mar 2025

https://github.com/jianhong/genomictools

docker file for genomic tools

bioinformatics-pipeline bwa chip-seq kallisto macs2 rna-seq salmon sleuth tximport

Last synced: 09 Mar 2026

https://github.com/crazyhottommy/chip-seq-carpentry

Development of the ChIPseq workshop for Data Carpentry

chip-seq data-carpentry genomics software-carpentry

Last synced: 07 Oct 2025

https://github.com/juliuspinsker/bioconductor-learning-container

🧬 Containerized development environment for Harvard's Professional Certificate in Data Analysis for Genomics (PH525.x series). Streamlined setup for Bioconductor, R, and genomic data analysis with RStudio and DevContainer support.

bioconductor bioinformatics chip-seq data-analysis data-science devcontainer dna-methylation docker edx functional-genomics genomics harvard harvardx ph525 ph525x r reproducible-research rna-seq rstudio single-cell-rna-seq

Last synced: 14 May 2026

https://github.com/anergictcell/wigfiles

chip-seq rna-seq wig

Last synced: 15 May 2026

https://github.com/openomics/hiip

An awesome Hi-C + ChIP (HiChIP) sequencing pipeline.

chip-seq hi-c hichip pipeline singularity snakemake

Last synced: 18 Jan 2026

https://github.com/stevekm/hic-bench-demo

Demo dataset & usage for HiC-Bench ChIP-Seq pipeline

chip-seq demo pipeline

Last synced: 04 Aug 2025

https://github.com/sebastian-gregoricchio/spacca

Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples

chip-seq chip-seq-analysis chip-seq-callers chip-seq-data chip-seq-peaks chipseq copynumber gatk gatk4 macs macs2 mutation mutation-analysis mutations normalization somatic-indels somatic-mutations somatic-variant somatic-variants

Last synced: 31 May 2026

https://github.com/sebastian-gregoricchio/rseb

An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.

atac-seq bedtools chip-seq cutandtag daily-tasks data-visualisation data-visualization datamining deeptools genomics ngs qpcr qpcr-analysis r rna-seq statistics