Cooler demo using a Jupyter notebook Binder
☆18Sep 24, 2020Updated 5 years ago
Alternatives and similar repositories for cooler-binder
Users that are interested in cooler-binder are comparing it to the libraries listed below
Sorting:
- ☆18Mar 12, 2024Updated last year
- snakemake pipeline for Hi-C post-processing☆22Jun 27, 2024Updated last year
- FreeHi-C pipeline for high fidelity Hi-C data simulation.☆12Jul 13, 2021Updated 4 years ago
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated last year
- A modular Hi-C mapping pipeline☆101Dec 5, 2024Updated last year
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆80Oct 31, 2024Updated last year
- The tools for your .cool's☆160Jul 7, 2025Updated 7 months ago
- Extract 3D contacts (.pairs) from sequencing alignments☆125Feb 3, 2026Updated last month
- Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.☆39May 3, 2025Updated 10 months ago
- Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.☆207May 19, 2018Updated 7 years ago
- HiGlass track for displaying arcs between disconnected regions☆10Dec 13, 2022Updated 3 years ago
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years ago
- A library to analyse the structure of 1d loops and simulate loop extrusion by loop extruding factors.☆11Feb 10, 2025Updated last year
- Plotting average TAD heatmap for Hi-C data (give TAD segmentation and cool/hiclib interactions map).☆10Jun 5, 2021Updated 4 years ago
- R package to evaluate reproducibility of Hi-C data☆10Mar 16, 2023Updated 2 years ago
- Software for comparing contact maps from HiC, CaptureC and other 3D genome data.☆26May 21, 2018Updated 7 years ago
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆67Jun 7, 2019Updated 6 years ago
- Fontanka is a set of tools to work with fountains in Hi-C data. It aims to provide a flexible Python API and specialized CLI for calling …☆13Dec 22, 2025Updated 2 months ago
- A cool place to store your Hi-C☆231Feb 23, 2026Updated last week
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆92Jan 28, 2025Updated last year
- Chromatin States Map in mouse embryonic stem cell☆19Apr 11, 2018Updated 7 years ago
- Tools for DLO HiC data analyze☆16Oct 31, 2022Updated 3 years ago
- Docker for 4DN Hi-C processing pipeline☆61Nov 26, 2024Updated last year
- Python bindings to UCSC BigWig and BigBed library☆36Jan 28, 2026Updated last month
- GENome Organisation Visual Analytics☆15Dec 24, 2021Updated 4 years ago
- Python bindings for hictk: read and write .cool and .hic files directly from Python☆16Updated this week
- A Python implementation of the original DI domain caller☆12Aug 2, 2020Updated 5 years ago
- Blazing fast toolkit to work with .hic and .cool files☆42Feb 23, 2026Updated last week
- An integrated package to process diploid Hi-C data☆17Dec 9, 2021Updated 4 years ago
- High-performance stochastic modeling of DNA loop extrusion interactions☆18Dec 22, 2025Updated 2 months ago
- HiCtrans is a pipeline to call translocations from Hi-C data☆17Sep 27, 2021Updated 4 years ago
- HiCSR: a Hi-C super-resolution framework for producing highly realistic contact maps☆15Nov 22, 2022Updated 3 years ago
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆41Jan 31, 2024Updated 2 years ago
- SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data☆42Jul 6, 2023Updated 2 years ago
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 2 years ago
- A toolkit for analyzing architectural stripes☆20Dec 1, 2024Updated last year
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆20Sep 12, 2023Updated 2 years ago
- A preprocessing and QC pipeline for HiChIP data☆40Jul 11, 2022Updated 3 years ago
- CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.☆23Jan 15, 2026Updated last month