Top 20 atac-seq open source projects

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

✭ 1,937

awesome-list data-visualization bioinformatics analysis clustering gene-expression dimensionality-reduction data-integration atac-seq single-cell rna-seq-data scrna-seq-data cell-cycle cell-differentiation gene-expression-profiles analysis-pipeline cell-populations rna-seq-experiments cell-clusters

reg-gen

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

✭ 64

python c shell CSS awk r bioinformatics dnase-seq genomics ngs chip-seq atac-seq footprinting differential-peak-calling

scABC

No description or website provided.

✭ 16

HTML r atac-seq single-cell single-cell-atac-seq

ataqv

A toolkit for QC and visualization of ATAC-seq results.

✭ 55

C++javascript HTML python CSS Makefile visualization quality-control tool software atac-seq

scATAC-benchmarking

Benchmarking computational single cell ATAC-seq methods

✭ 137

Jupyter Notebook benchmark reproducible atac-seq singlecell jupyternotebook

pyflow-ATACseq

ATAC-seq snakemake pipeline

✭ 61

python shell snakemake atac-seq

ATACseq

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

✭ 51

shell r python Makefile Dockerfile sequencing next-generation-sequencing atac-seq chromatin nucleosome-positioning peak-detection atac-seq-pipeline

NucleoATAC

nucleosome calling using ATAC-seq

✭ 95

python bioinformatics atac-seq nuclesosome

gchromVAR

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

✭ 31

r gwas epigenetics atac-seq single-cell

ATAC-seq

Basic workflow for ATAC-seq analysis

✭ 30

r shell unix atac-seq

GGR-cwl

CWL tools and workflows for GGR

✭ 20

Common Workflow Language python Jinja shell dnase-seq rna-seq chip-seq atac-seq cwl

PECA

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

✭ 31

matlab shell dnase-seq rna-seq gene-expression atac-seq gene-regulatory-network chromatin-accessibiity

atacr

Analysing Capture Seq Count Data

✭ 14

r science data bioinformatics genomics analysis capture rnaseq atac-seq count-data

ALPS

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

✭ 13

r dataviz rstats bioconductor data-analysis chip-seq atac-seq wgbs epigenomics

dolphinnext

A graphical user interface for distributed data processing of high throughput genomics

✭ 92

PHP javascript Nextflow CSS hack Twig bioinformatics rna-seq pipeline drag-and-drop pipelines chip-seq atac-seq clusters workflows amazon-cloud dolphinnext share-pipelines

Protocols-4pub

Multi-omics analysis protocols by Lyu.

✭ 37

HTML r rna-seq chip-seq atac-seq wgbs

TOBIAS

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

✭ 128

python cython shell bioinformatics atac-seq footprinting

scATAC-pro

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

✭ 63

r shell perl Makefile python bioinformatics pipeline atac-seq single-cell chromatin-accessibiity

chromVAR

chromatin Variability Across Regions (of the genome!)

✭ 116

r C++bioinformatics dnase-seq atac-seq

HMMRATAC

HMMRATAC peak caller for ATAC-seq data

✭ 86

java shell machine-learning sequencing peak-caller atac-seq peak-detection

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