ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization
☆29Aug 13, 2021Updated 4 years ago
Alternatives and similar repositories for ChIA-PIPE
Users that are interested in ChIA-PIPE are comparing it to the libraries listed below
Sorting:
- ☆12Aug 28, 2020Updated 5 years ago
- ChIA-PET Utilities☆13Dec 19, 2021Updated 4 years ago
- a versatile and flexible pipeline for analysing different variants of ChIA-PET data☆36Nov 25, 2024Updated last year
- ChIA-PET, HiChIP, PLAC-Seq data analysis, with linker detection, linker filter, or restriction process for HiChIP, mapping, call cluster …☆22Jul 19, 2024Updated last year
- chia pet analysis software☆25Jan 17, 2019Updated 7 years ago
- 🍹This repo includes the scripts and analysis notebook for the Droplet Hi-C manuscript☆15Feb 6, 2026Updated 3 weeks ago
- General analysis of HiC data, including compartment A/B, domains and loops.☆14Feb 17, 2023Updated 3 years ago
- Chromatin States Map in mouse embryonic stem cell☆19Apr 11, 2018Updated 7 years ago
- an R/Shiny application for interactive creation of non-circular plots of whole genomes☆45May 15, 2025Updated 9 months ago
- Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.☆52Jun 17, 2025Updated 8 months ago
- Statistically Significant loops from HiChIP data☆46Apr 17, 2024Updated last year
- ☆18Jul 15, 2025Updated 7 months ago
- DeepTACT: predicting three-dimensional chromatin contacts via bootstrapping deep learning☆20Jul 23, 2020Updated 5 years ago
- EpiGenome Gateway - WashU EpiGenome Browser☆21Oct 11, 2021Updated 4 years ago
- A self-contained repository of all code needed for SPRITE analysis☆21Jul 28, 2021Updated 4 years ago
- Python library for processing and visualizing Hi-C data☆20May 31, 2020Updated 5 years ago
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆475Aug 31, 2025Updated 6 months ago
- A preprocessing and QC pipeline for HiChIP data☆40Jul 11, 2022Updated 3 years ago
- HiC-Reg is a tool to predict Hi-C contact counts from one-dimensional regulatory signals☆11Aug 25, 2020Updated 5 years ago
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 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…☆108Nov 12, 2025Updated 3 months ago
- Genome-wide contact analysis using sklearn☆72Mar 23, 2024Updated last year
- ☆70Nov 21, 2025Updated 3 months ago
- WashU Epigenome Browser☆76Mar 18, 2025Updated 11 months ago
- Single-cell Hi-C data analysis toolbox☆27Aug 13, 2021Updated 4 years ago
- Chromatin State Maps in Mouse☆23May 16, 2018Updated 7 years ago
- An Optimized Nested TAD caller for Hi-C data☆25Jun 30, 2021Updated 4 years ago
- Multi-omics analysis protocols by Lyu.☆53Aug 22, 2023Updated 2 years ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆92Oct 29, 2025Updated 4 months ago
- multiway chromatin interaction, 3D genome, single-nucleus, hypergraph representation learning☆31Jul 20, 2022Updated 3 years ago
- Project bulk/single-cell RNA-seq data to given LSI space☆11Jan 17, 2022Updated 4 years ago
- Particle dynamics and simulated annealing for chromosome structure calculation☆28Mar 15, 2024Updated last year
- A 3D genome data processing tutorial for ISMB/ECCB 2017☆52Jul 21, 2017Updated 8 years ago
- Pore-C support☆54Feb 22, 2023Updated 3 years ago
- A collection of tools for Hi-C data analysis☆631Jan 31, 2026Updated last month
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆431Mar 28, 2024Updated last year
- A machine-learning algorithm to predict CTCF-mediated long-range chromatin interactions☆17Nov 7, 2018Updated 7 years ago
- an efficient Hi-C data processing pipeline☆17Mar 26, 2024Updated last year
- Python bindings for hictk: read and write .cool and .hic files directly from Python☆16Feb 23, 2026Updated last week