A Python implementation for BH-FDR and HiCCUPS
☆54Dec 29, 2025Updated 2 months ago
Alternatives and similar repositories for HiCPeaks
Users that are interested in HiCPeaks are comparing it to the libraries listed below
Sorting:
- Genome-wide contact analysis using sklearn☆73Mar 23, 2024Updated last year
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 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
- An easy-to-use Hi-C data processing software supporting distributed computation.☆62Aug 6, 2024Updated last year
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆77Jul 22, 2025Updated 7 months ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆80Jan 24, 2025Updated last year
- Python bindings for hictk: read and write .cool and .hic files directly from Python☆16Mar 2, 2026Updated last week
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆69Dec 16, 2022Updated 3 years ago
- A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes☆75Oct 21, 2023Updated 2 years ago
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years ago
- Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the…☆23Jun 4, 2023Updated 2 years ago
- An integrated package to process diploid Hi-C data☆17Dec 9, 2021Updated 4 years ago
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆80Oct 31, 2024Updated last year
- Data and the co-authored network I extracted for lab selection in 3D genome research field☆16Dec 26, 2021Updated 4 years ago
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 2 years ago
- R package to evaluate the reproducibility of Hi-C data☆27Jun 23, 2023Updated 2 years ago
- TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.☆49Nov 16, 2022Updated 3 years ago
- An Optimized Nested TAD caller for Hi-C data☆25Jun 30, 2021Updated 4 years ago
- FAN-C: Framework for the ANalysis of C-like data☆122Mar 13, 2024Updated last year
- The tools for your .cool's☆160Jul 7, 2025Updated 8 months ago
- GENome Organisation Visual Analytics☆15Dec 24, 2021Updated 4 years ago
- Python bindings to UCSC BigWig and BigBed library☆36Mar 2, 2026Updated last week
- Lightweight converter between hic and cool contact matrices.☆75Jul 15, 2024Updated last year
- Software for comparing contact maps from HiC, CaptureC and other 3D genome data.☆26May 21, 2018Updated 7 years ago
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆92Jan 28, 2025Updated last year
- A toolkit for analyzing architectural stripes☆20Dec 1, 2024Updated last year
- Red-C data processing☆15Apr 18, 2023Updated 2 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 …☆14Dec 22, 2025Updated 2 months ago
- Fast alignment and preprocessing of chromatin profiles☆214Jan 17, 2026Updated last month
- A set of pipelines for Hi-C and ChIP-Seq analysis.☆48Apr 11, 2024Updated last year
- Extract 3D contacts (.pairs) from sequencing alignments☆125Feb 3, 2026Updated last month
- Extract data quickly from Juicebox via straw☆69Apr 6, 2025Updated 11 months ago
- Accurate and flexible loops calling tool for 3D genomic data.☆114May 19, 2022Updated 3 years ago
- Comparison of Hi-C Experiments using Structural Similarity.☆28Jul 18, 2023Updated 2 years ago
- QC report generator for Hi-C pairs file☆13Sep 14, 2020Updated 5 years ago
- A preprocessing and QC pipeline for HiChIP data☆40Jul 11, 2022Updated 3 years ago
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆268Jul 17, 2025Updated 7 months ago
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆67Jun 7, 2019Updated 6 years ago
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆21May 11, 2023Updated 2 years ago