Here are
90 public repositories
matching this 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
Updated
Jul 7, 2020
Python
Customizable workflows based on snakemake and python for the analysis of NGS data
Updated
Sep 11, 2020
Python
ATAC-seq and DNase-seq processing pipeline
Updated
Sep 25, 2019
Python
nucleosome calling using ATAC-seq
Updated
Mar 7, 2019
Python
Benchmarking computational single cell ATAC-seq methods
Updated
Feb 19, 2020
Jupyter Notebook
chromatin Variability Across Regions (of the genome!)
HMMRATAC peak caller for ATAC-seq data
A graphical user interface for distributed data processing of high throughput genomics
Updated
Jul 22, 2020
JavaScript
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Updated
Sep 11, 2020
Python
ATAC-seq peak-calling, QC and differential analysis pipeline
Updated
Aug 18, 2020
Nextflow
A toolkit for QC and visualization of ATAC-seq results.
ATAC-seq snakemake pipeline
Updated
Feb 13, 2020
Python
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
Updated
Sep 9, 2020
Python
Analysis pipelines for sequencing data
Updated
Sep 10, 2020
Shell
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and RNA-seq workflows. Works equally easy with public as local data.
Updated
Sep 18, 2020
Python
Scasat is a single cell ATAC-seq preprocessing and analysis pipeline
Updated
Feb 27, 2019
Jupyter Notebook
A small R package to make sequencing read coverage plots in R.
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
Updated
Aug 5, 2020
Shell
deepStats: a stastitical toolbox for deeptools and genomic signals
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
A toolkit for working with ATAC-seq data.
Updated
Sep 17, 2019
Python
Bioconductor package esATAC: an Easy-to-use Systematic pipeline for ATAC-seq data analysis
CWL tools and workflows for GGR
Updated
Sep 14, 2020
Common Workflow Language
ATAC-seq lab for BIOINF545
Updated
Mar 22, 2019
Shell
A Python package for fast operations on 1-dimensional genomic signal tracks
Updated
Apr 3, 2020
Python
Analysing Capture Seq Count Data
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
Updated
Mar 3, 2020
MATLAB
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