atac-seq
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Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
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Oct 23, 2025
MACS -- Model-based Analysis of ChIP-Seq
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Nov 27, 2025 - Python
🎯 ChIP peak Annotation, Comparison and Visualization
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Nov 4, 2025 - R
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
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Dec 2, 2025 - Python
Benchmarking computational single cell ATAC-seq methods
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Nov 30, 2020 - Jupyter Notebook
chromatin Variability Across Regions (of the genome!)
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Jul 10, 2024 - R
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.
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Nov 22, 2025 - Python
ATAC-seq and DNase-seq processing pipeline
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Jun 21, 2022 - Python
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
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Nov 3, 2025 - Python
HMMRATAC peak caller for ATAC-seq data
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Nov 12, 2024 - Java
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
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Nov 25, 2025 - Python
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
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Dec 11, 2025 - Nextflow
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
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Mar 6, 2025 - R
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
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Aug 3, 2023 - Shell
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