HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
☆446Mar 28, 2024Updated 2 years ago
Alternatives and similar repositories for HiC-Pro
Users that are interested in HiC-Pro are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆490Sep 15, 2026Updated 3 weeks ago
- “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau☆190Jul 13, 2020Updated 6 years ago
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆279Sep 24, 2026Updated 2 weeks ago
- Visualization and analysis software for Hi-C data -☆305Sep 2, 2026Updated last month
- Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…☆96Aug 29, 2022Updated 4 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- A collection of tools for Hi-C data analysis☆653Oct 3, 2026Updated last week
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated 2 years ago
- 3D de novo assembly (3D DNA) pipeline☆231Nov 29, 2023Updated 2 years ago
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆68Jun 7, 2019Updated 7 years ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆180Oct 20, 2024Updated last year
- A cool place to store your Hi-C☆245Oct 5, 2026Updated last week
- A preprocessing and QC pipeline for HiChIP data☆40Jul 11, 2022Updated 4 years ago
- TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FAST…☆113Nov 12, 2025Updated 11 months ago
- chia pet analysis software☆25Jan 17, 2019Updated 7 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)☆80Oct 12, 2018Updated 8 years ago
- Extract 3D contacts (.pairs) from sequencing alignments☆138Jul 29, 2026Updated 2 months ago
- The tools for your .cool's☆171Mar 19, 2026Updated 6 months ago
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆82Oct 31, 2024Updated last year
- Fast alignment and preprocessing of chromatin profiles☆229Mar 20, 2026Updated 6 months ago
- Python library to facilitate genome assembly, annotation, and comparative genomics☆932Sep 19, 2026Updated 3 weeks ago
- Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.☆214May 19, 2018Updated 8 years ago
- A modular Hi-C mapping pipeline☆106Dec 5, 2024Updated last year
- FAN-C: Framework for the ANalysis of C-like data☆120Mar 13, 2024Updated 2 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆220Jun 30, 2026Updated 3 months ago
- Software to compute reproducibility and quality scores for Hi-C data☆52Apr 12, 2019Updated 7 years ago
- python module to plot beautiful and highly customizable genome browser tracks☆905Oct 3, 2026Updated last week
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆84Jan 24, 2025Updated last year
- TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C☆121Jan 8, 2026Updated 9 months ago
- a versatile and flexible pipeline for analysing different variants of ChIA-PET data☆36Nov 25, 2024Updated last year
- R package to evaluate reproducibility of Hi-C data☆10Mar 16, 2023Updated 3 years ago
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆816May 31, 2026Updated 4 months ago
- Statistically Significant loops from HiChIP data☆49Apr 17, 2024Updated 2 years ago
- AI Agents on 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.
- “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau☆21Jul 13, 2020Updated 6 years ago
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 3 years ago
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆189May 17, 2024Updated 2 years ago
- Tools to process and analyze deep sequencing data.☆768Sep 27, 2026Updated 2 weeks ago
- PASA software☆204Feb 12, 2025Updated last year
- 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
- GENome Organisation Visual Analytics☆91Feb 3, 2026Updated 8 months ago