Search Packages

macs2

MACS -- Model-based Analysis of ChIP-Seq

macs3

MACS -- Model-based Analysis of ChIP-Seq

rocco

Robust Open Chromatin Detection via Convex Optimization: Multisample Consensus Peak Calling

atacfragqc

QC for ATAC-seq fragments

circe-py

Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.

rgt

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

tobias

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

bintogene

A tool for replacing promoter accessibility with a gene activity score.

ngs-toolkit

A toolkit for NGS analysis with Python

recon

Exploring multicellular coordination from single-cell gene expression / multi-omics using mutlilayer network representations

zen-norm

Zone Equalisation Normalisation: A Python package for bigWig scaling

pybedgraph

A Python package for fast operations on 1-dimensional genomic signal tracks

fseq2

Improving the feature density based peak caller with dynamic statistics

asap-o-matic

Rearrange ASAP-seq antibody reads into something Alevin can recognize and count.

maxatac

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

nucleoatac

nucleosome calling using ATAC-seq

chame

Chromatin analysis module

cisvar

Calculate both pre and post frequencies for ChIP or ATAC style data