chip-seq
There are 244 repositories under chip-seq topic.
crazyhottommy/ChIP-seq-analysis
ChIP-seq analysis notes from Ming Tang
macs3-project/MACS
MACS -- Model-based Analysis of ChIP-Seq
deeptools/deepTools
Tools to process and analyze deep sequencing data.
maxplanck-ie/snakepipes
Customizable workflows based on snakemake and python for the analysis of NGS data
galaxyproject/training-material
A collection of Galaxy-related training material
YuLab-SMU/ChIPseeker
:dart: ChIP peak Annotation, Comparison and Visualization
nf-core/chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
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.
harbourlab/SparK
Publication quality NGS track plotting
CostaLab/reg-gen
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
crazyhottommy/pyflow-ChIPseq
a snakemake pipeline to process ChIP-seq files from GEO or in-house
kundajelab/chipseq_pipeline
AQUAS TF and histone ChIP-seq pipeline
nf-core/differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
sajuukLyu/Protocols-4pub
Multi-omics analysis protocols by Lyu.
dputhier/pygtftk
A python package and a set of shell commands to handle GTF files
pinellolab/haystack_bio
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
pbenner/gonetics
Go / Golang Bioinformatics Library
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.
junjunlab/BioSeqUtils
Extract Sequence from Genome According to Annotation File
gtrichard/deepStats
deepStats: a stastitical toolbox for deeptools and genomic signals
JetBrains-Research/bioinf-commons
Bioinformatics library in Kotlin
tushiqi/MAnorm2
MAnorm2 for Normalizing and Comparing ChIP-seq Samples
biocore-ntnu/epic
(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
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.
MiraldiLab/maxATAC
Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
tjparnell/biotoolbox
Tools for querying and analysis of genomic data
bioinformatics-core-shared-training/cruk-summer-school-2018
Summer school course materials collection
TheJacksonLaboratory/pyBedGraph
A Python package for fast operations on 1-dimensional genomic signal tracks
Bohdan-Khomtchouk/Microscope
ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps
shao-lab/MAnorm
A robust model for quantitative comparison of ChIP-Seq data sets.
Duke-GCB/GGR-cwl
CWL tools and workflows for GGR
epigen/open_pipelines
Pipelines for NGS data preprocessing by the Bock lab and friends
Genometric/MSPC
Using combined evidence from replicates to evaluate ChIP-seq peaks
guigolab/chip-nf
An automated ChIP-seq pipeline using Nextfow
robertamezquita/marge
API for HOMER in R for Genomic Analysis using Tidy Conventions
eblancoga/seqcode
Suite of command-line software for high-performance graphical analysis of ChIP-seq/RNA-seq/ATAC-seq data