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

MACS -- Model-based Analysis of ChIP-Seq

ATAC-seq peak-calling and QC analysis pipeline

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

ATAC-seq and DNase-seq processing pipeline

🎯 ChIP peak Annotation, Comparison and Visualization

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

Benchmarking computational single cell ATAC-seq methods

chromatin Variability Across Regions (of the genome!)

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

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

Basic workflow for ATAC-seq analysis

nucleosome calling using ATAC-seq

ATAC-seq snakemake pipeline

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

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.

Analysis pipelines for genomic sequencing data

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

HMMRATAC peak caller for ATAC-seq data

A small R package to make sequencing read coverage plots in R.