CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hierarchical organization and obtain sub-compartments; (3) compute nested sub-domains within each chromatin domain from short-range contacts.
☆26Apr 16, 2025Updated 11 months ago
Alternatives and similar repositories for CALDER2
Users that are interested in CALDER2 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆22Jul 27, 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 3 months ago
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆22May 11, 2023Updated 2 years ago
- A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.☆14Mar 9, 2023Updated 3 years ago
- Genome-wide contact analysis using sklearn☆74Mar 23, 2024Updated 2 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- R package to evaluate the reproducibility of Hi-C data☆27Jun 23, 2023Updated 2 years ago
- FAN-C: Framework for the ANalysis of C-like data☆120Mar 13, 2024Updated 2 years ago
- GENome Organisation Visual Analytics☆86Feb 3, 2026Updated 2 months ago
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 3 years ago
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 3 months ago
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆268Jul 17, 2025Updated 8 months ago
- ☆17May 30, 2022Updated 3 years ago
- ☆52Mar 17, 2023Updated 3 years ago
- dcHiC: Differential compartment analysis for Hi-C datasets☆75Jan 10, 2024Updated 2 years ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated last year
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆81Jan 24, 2025Updated last year
- ☆14Mar 28, 2025Updated last year
- Interspecies Point Projection - A tool for comparative genomics beyond alignable sequence☆26Feb 9, 2026Updated 2 months ago
- DiffDomain is a statistically sound method for detecting differential TADs between conditions☆17Jun 27, 2025Updated 9 months ago
- Extract 3D contacts (.pairs) from sequencing alignments☆129Feb 3, 2026Updated 2 months ago
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years ago
- Blazing fast toolkit to work with .hic and .cool files☆44Updated this week
- ☆16Dec 25, 2024Updated last year
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps☆61Aug 28, 2025Updated 7 months ago
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Dec 16, 2022Updated 3 years ago
- Docker for 4DN Hi-C processing pipeline☆61Nov 26, 2024Updated last year
- R functions for very fast eigenvector calculation☆11Jan 18, 2023Updated 3 years ago
- Package for analysis and characterization of differential TADs☆27Apr 25, 2022Updated 3 years ago
- A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes☆76Oct 21, 2023Updated 2 years ago
- 3DGB is a workflow to build 3D models of genomes from HiC data☆13Jan 26, 2026Updated 2 months ago
- R package to draw syntenic plots in 3 different styles☆46Feb 2, 2026Updated 2 months ago
- Code associated with with the 2023 Nature Genetics Paper "Region Capture Micro-C reveals coalescence of enhancers and promoters into nest…☆12May 31, 2023Updated 2 years ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- A cool place to store your Hi-C☆234Updated this week
- ☆21Apr 23, 2024Updated last year
- ☆29Apr 23, 2025Updated 11 months ago
- An Optimized Nested TAD caller for Hi-C data☆25Jun 30, 2021Updated 4 years ago
- GENome Organisation Visual Analytics☆15Dec 24, 2021Updated 4 years ago
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆84Mar 22, 2026Updated 2 weeks ago
- snakemake pipeline for Hi-C post-processing☆22Jun 27, 2024Updated last year