Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
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Updated
Aug 16, 2024
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
🎯 ChIP peak Annotation, Comparison and Visualization
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
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!)
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
HMMRATAC peak caller for ATAC-seq data
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
A toolkit for QC and visualization of ATAC-seq results.
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
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