Hi-C data processing pipeline
☆42Feb 27, 2024Updated 2 years ago
Alternatives and similar repositories for HiCUP
Users that are interested in HiCUP are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- 3DGB is a workflow to build 3D models of genomes from HiC data☆13May 6, 2026Updated 4 months ago
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆23Sep 1, 2026Updated 2 weeks ago
- Joint normalization of multiple Hi-C matrices, visualization and detection of differential chromatin interactions, supporting covariates.☆10Jul 9, 2026Updated 2 months ago
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆490Updated this week
- Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the…☆22Updated this week
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- HiCAT new project☆39May 18, 2025Updated last year
- An effective alignment tool for long noisy 3C data (e.g. Pore-C and C-walk)☆16Oct 23, 2024Updated last year
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆444Mar 28, 2024Updated 2 years ago
- Extract 3D contacts (.pairs) from sequencing alignments☆138Jul 29, 2026Updated last month
- A filter algorithm with program to filter an alignment or mapping file☆12May 15, 2025Updated last year
- 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
- Yet another Hi-C scaffolding tool☆183Nov 4, 2024Updated last year
- A command line tool to compute mapping statistics from a BAM file☆25Mar 7, 2022Updated 4 years ago
- ☆42May 19, 2025Updated last year
- 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.
- Accurate haplotype construction and detection of selection signatures enabled by 889 high quality pig genome sequences☆14May 11, 2023Updated 3 years ago
- an efficient Hi-C data processing pipeline☆20Mar 26, 2024Updated 2 years ago
- ☆88Jul 12, 2024Updated 2 years ago
- HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.☆277Jul 17, 2025Updated last year
- ☆22Aug 11, 2020Updated 6 years ago
- A novel genome assembly pipeline based on deep learning☆71Dec 2, 2024Updated last year
- HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C☆26Jan 14, 2021Updated 5 years ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆180Oct 20, 2024Updated last year
- TransposonPSI involves a PSI-blast search of a protein or nucleotide sequence against a set of profiles of proteins corresponding to majo…☆14Apr 28, 2020Updated 6 years ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Tools for DLO HiC data analyze☆16Oct 31, 2022Updated 3 years ago
- ☆13Sep 4, 2025Updated last year
- A Generalizable Model for 3D Chromosome Reconstruction Using Graph Convolutional Neural Networks☆18Sep 9, 2021Updated 5 years ago
- ☆21Jan 1, 2022Updated 4 years ago
- isoCirc☆10Nov 27, 2023Updated 2 years ago
- Detecting contamination in NGS data and multi-species analysis☆89Nov 7, 2025Updated 10 months ago
- Chromatin contact paired-read single-cell Hi-C processing module for Nuc3D and NucTools☆15Sep 15, 2025Updated last year
- ☆13Jul 21, 2021Updated 5 years ago
- A software suite for Probe Design and Proximity Detection for targeted chromosome conformation capture applications☆13Feb 28, 2026Updated 6 months 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.
- ☆15Apr 16, 2026Updated 5 months ago
- A Hi-C scaffolding method☆22Dec 22, 2021Updated 4 years ago
- ☆39Aug 14, 2019Updated 7 years ago
- Extract data quickly from Juicebox via straw☆70Apr 6, 2025Updated last year
- 3D de novo assembly (3D DNA) pipeline☆229Nov 29, 2023Updated 2 years ago
- Software to compute reproducibility and quality scores for Hi-C data☆52Apr 12, 2019Updated 7 years ago
- software tools for haplotype assembly from sequence data☆233Feb 9, 2025Updated last year