atac-seq
There are 181 repositories under atac-seq topic.
seandavi/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
macs3-project/MACS
MACS -- Model-based Analysis of ChIP-Seq
maxplanck-ie/snakepipes
Customizable workflows based on snakemake and python for the analysis of NGS data
YuLab-SMU/ChIPseeker
:dart: ChIP peak Annotation, Comparison and Visualization
loosolab/TOBIAS
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
nf-core/atacseq
ATAC-seq peak-calling and QC analysis pipeline
pinellolab/scATAC-benchmarking
Benchmarking computational single cell ATAC-seq methods
GreenleafLab/chromVAR
chromatin Variability Across Regions (of the genome!)
kundajelab/atac_dnase_pipelines
ATAC-seq and DNase-seq processing 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.
CostaLab/reg-gen
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
GreenleafLab/NucleoATAC
nucleosome calling using ATAC-seq
LiuLabUB/HMMRATAC
HMMRATAC peak caller for ATAC-seq data
crazyhottommy/pyflow-ATACseq
ATAC-seq snakemake pipeline
nf-core/differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
wbaopaul/scATAC-pro
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
reskejak/ATAC-seq
Basic workflow for ATAC-seq analysis
tobiasrausch/ATACseq
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
igordot/sns
Analysis pipelines for genomic sequencing data
ParkerLab/ataqv
A toolkit for QC and visualization of ATAC-seq results.
epigen/atacseq_pipeline
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
sajuukLyu/Protocols-4pub
Multi-omics analysis protocols by Lyu.
caleblareau/gchromVAR
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
SUwonglab/PECA
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
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
kauralasoo/wiggleplotr
A small R package to make sequencing read coverage plots in R.
ManchesterBioinference/Scasat
Scasat is a single cell ATAC-seq preprocessing and analysis pipeline
gtrichard/deepStats
deepStats: a stastitical toolbox for deeptools and genomic signals
ay-lab/ATACProc
ATAC-seq processing pipeline
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
jiang-junyao/IReNA
R package IReNA
aertslab/PUMATAC
Pipeline for Universal Mapping of ATAC-seq
ParkerLab/bioinf545
ATAC-seq lab for BIOINF545
TheJacksonLaboratory/pyBedGraph
A Python package for fast operations on 1-dimensional genomic signal tracks