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.
☆28Jul 23, 2026Updated 3 weeks 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:
- ☆23Jul 27, 2023Updated 3 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 7 months ago
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆23May 11, 2023Updated 3 years ago
- A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.☆15Apr 24, 2026Updated 3 months ago
- A cross-platform method for chromatin contact normalization☆16Dec 29, 2025Updated 7 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Genome-wide contact analysis using sklearn☆76Mar 23, 2024Updated 2 years ago
- R package to evaluate the reproducibility of Hi-C data☆28Jun 23, 2023Updated 3 years ago
- GENome Organisation Visual Analytics☆92Feb 3, 2026Updated 6 months ago
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 4 years ago
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 7 months ago
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆275Jul 17, 2025Updated last year
- dcHiC: Differential compartment analysis for Hi-C datasets☆74Jan 10, 2024Updated 2 years ago
- ☆17May 30, 2022Updated 4 years ago
- ☆52Mar 17, 2023Updated 3 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated 2 years ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆83Jan 24, 2025Updated last year
- ☆14Mar 28, 2025Updated last year
- Extract 3D contacts (.pairs) from sequencing alignments☆137Jul 29, 2026Updated 2 weeks ago
- DiffDomain is a statistically sound method for detecting differential TADs between conditions☆18Jun 27, 2025Updated last year
- ☆21Apr 23, 2024Updated 2 years ago
- Blazing fast toolkit to work with .hic and .cool files☆45Updated this week
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years ago
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Jul 7, 2026Updated last month
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps☆63Aug 28, 2025Updated 11 months ago
- ☆15Apr 16, 2026Updated 3 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 3 years ago
- R package to draw syntenic plots in 3 different styles☆46Feb 2, 2026Updated 6 months ago
- Docker for 4DN Hi-C processing pipeline☆62Nov 26, 2024Updated last year
- 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
- R functions for very fast eigenvector calculation☆11Jan 18, 2023Updated 3 years ago
- PPL (Pore-C PipLine) is a set of tools to process, evaluate and visualize the multi-way contacts experiment based on 3C and ONT long read…☆16Apr 22, 2025Updated last year
- Package for analysis and characterization of differential TADs☆27Jul 15, 2026Updated 3 weeks ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- 3DGB is a workflow to build 3D models of genomes from HiC data☆13May 6, 2026Updated 3 months ago
- ☆29Apr 23, 2025Updated last year
- A cool place to store your Hi-C☆242Updated this week
- SIP: Significant Interaction Peak caller☆17Apr 24, 2025Updated last year
- snakemake pipeline for Hi-C post-processing☆22Jun 27, 2024Updated 2 years ago
- An Optimized Nested TAD caller for Hi-C data☆26Jun 30, 2021Updated 5 years ago
- GENome Organisation Visual Analytics☆16Dec 24, 2021Updated 4 years ago