Reverse Dependencies of cooler

The following projects have a declared dependency on cooler:

• allcools — Toolkit for single-cell DNA methylome and multiomic data analysis.
• capcruncher — An end-to-end solution for processing Capture-C, Tri-C and Tiled-C data
• chromosight — Detect loops (and other patterns) in Hi-C contact maps.
• clodius — Tile generation for big data
• coolbox — Jupyter notebook based genomic data visulization toolkit.
• coolpuppy — A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
• DeCGR — An interactive toolkit for deciphering CGRs from Hi-C data
• DiffDomain-py3 — DiffDomain can test the significant difference of TADs on chromatin.
• FIREcaller — Python library for detecting Frequently Interacting REgions (FIREs) from Hi-C data
• hic2cool — Converter between hic files (from juicer) and single-resolution or multi-resolution cool files (for cooler). Both hic and cool files describe Hi-C contact matrices. Intended to be lightweight, this can be used as an imported package or a stand-alone Python tool for command line conversion.
• HiCExplorer — Set of programs to process, analyze and visualize Hi-C data
• hiclip — no summary
• HiCMatrix — Helper package which implements HiCMatrix class for HiCExplorer, pyGenomeTracks and scHiCExplorer.
• HiCPlot — plot heatmaps from Hi-C matrix and tracks from bigwig files
• hicrep — Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with sparse contact matrix support
• hicreppy — Reimplementation of the hicrep with added support for sparse matrix and multiple chromosomes.
• hicstuff — General purpose stuff to generate and handle Hi-C data in its simplest form.
• hictools — Tools for handling hic data
• HiNT-Package — HiNT -- HiC for copy number vairations and translocations detection
• HiSTra — Spectral translocation detection of HiC matrices.
• hisv — A computational pipeline for structural variation detection from Hi-C data
• mustache-hic — Mustache is a Hi-C analysis tool
• nucbox — Ultra fast chromosome 3D reconstraction.
• py3dpolys-le — 3D Polymer Simulations - Loop Extrusion model
• sc3dg — A toolkit for processing single cell Hi-C data
• schickit — a toolkit for processing single cell Hi-C data
• selfish-hic — Hi-C Differential Analysis software created and maintained by the Ay Lab
• stripenn — Image-processing based detection of architectural stripes from chromatin conformation data
• TADGATE — A versatile framework to uncover topologically associating domains from three-dimensional genome maps
• trackC — no summary