There are 11 repositories under atac-seq topic.
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
Customizable workflows based on snakemake and python for the analysis of NGS data
:dart: ChIP peak Annotation, Comparison and Visualization
Benchmarking computational single cell ATAC-seq methods
ATAC-seq and DNase-seq processing pipeline
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.
chromatin Variability Across Regions (of the genome!)
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
Scasat is a single cell ATAC-seq preprocessing and analysis pipeline
A small R package to make sequencing read coverage plots in R.
Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using bash and Python.
Extract Sequence from Genome According to Annotation File
Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
A Python package for fast operations on 1-dimensional genomic signal tracks