Simple codes and lines to process 3C/Hi-C data
☆18Oct 21, 2021Updated 4 years ago
Alternatives and similar repositories for 3C_tutorial
Users that are interested in 3C_tutorial are comparing it to the libraries listed below
Sorting:
- 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 2 months ago
- Simple library/pipeline to generate and handle Hi-C data.☆39Feb 13, 2026Updated last month
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 2 years ago
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years ago
- Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.☆39Updated this week
- 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
- A preprocessing and QC pipeline for HiChIP data☆40Jul 11, 2022Updated 3 years ago
- Software for comparing contact maps from HiC, CaptureC and other 3D genome data.☆26May 21, 2018Updated 7 years ago
- Tools for DLO HiC data analyze☆16Oct 31, 2022Updated 3 years ago
- Relates to the article by Lioy, Cournac et al., Cell, 2018 (Functional partitioning of a bacterial chromosome through the interplay of nu…☆11Aug 19, 2020Updated 5 years ago
- Red-C data processing☆15Apr 18, 2023Updated 2 years ago
- Comparison of Hi-C Experiments using Structural Similarity.☆28Jul 18, 2023Updated 2 years ago
- FAN-C: Framework for the ANalysis of C-like data☆122Mar 13, 2024Updated 2 years ago
- A 3D genome data processing tutorial for ISMB/ECCB 2017☆52Jul 21, 2017Updated 8 years ago
- R package to evaluate reproducibility of Hi-C data☆10Mar 16, 2023Updated 3 years ago
- A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.☆14Mar 9, 2023Updated 3 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…☆109Nov 12, 2025Updated 4 months ago
- dcHiC: Differential compartment analysis for Hi-C datasets☆74Jan 10, 2024Updated 2 years ago
- Lightweight converter between hic and cool contact matrices.☆75Jul 15, 2024Updated last year
- A Generalizable Model for 3D Chromosome Reconstruction Using Graph Convolutional Neural Networks☆18Sep 9, 2021Updated 4 years ago
- ☆52Mar 17, 2023Updated 3 years ago
- ☆12Jun 16, 2023Updated 2 years ago
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Dec 16, 2022Updated 3 years ago
- Scripts for the analysis of TT-seq and DRB/TT-seq data.☆11Mar 11, 2020Updated 6 years ago
- GENome Organisation Visual Analytics☆15Dec 24, 2021Updated 4 years ago
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆41Jan 31, 2024Updated 2 years ago
- French Reproducibility Network website☆11Updated this week
- Python bindings for hictk: read and write .cool and .hic files directly from Python☆16Updated this week
- A self-contained repository of all code needed for SPRITE analysis☆21Jul 28, 2021Updated 4 years ago
- an efficient data integration method for multiple spatial transcriptomics data with non- cluster-relevant effects such as the complex batc…☆12Dec 15, 2025Updated 3 months ago
- Architectural stripe detection from 3D genome conformation data☆18Sep 15, 2025Updated 6 months ago
- Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.☆207May 19, 2018Updated 7 years ago
- Hi-C data super-resolution with generative adversarial networks☆15Jul 6, 2021Updated 4 years ago
- personal genome constructor☆10May 29, 2025Updated 9 months ago
- Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)☆20Jul 10, 2024Updated last year
- A toolkit for analyzing architectural stripes☆20Dec 1, 2024Updated last year
- Common utilities to ease the development of Python packages☆12Mar 2, 2026Updated 2 weeks ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆20Sep 12, 2023Updated 2 years ago
- Single-cell Hi-C data analysis toolbox☆27Aug 13, 2021Updated 4 years ago