Joint normalization of multiple Hi-C matrices, visualization and detection of differential chromatin interactions, supporting covariates.
☆10Apr 22, 2022Updated 3 years ago
Alternatives and similar repositories for multiHiCcompare
Users that are interested in multiHiCcompare are comparing it to the libraries listed below
Sorting:
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years ago
- Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the…☆23Jun 4, 2023Updated 2 years ago
- DiffDomain is a statistically sound method for detecting differential TADs between conditions☆17Jun 27, 2025Updated 8 months ago
- A toolkit for analyzing architectural stripes☆20Dec 1, 2024Updated last year
- 3DGB is a workflow to build 3D models of genomes from HiC data☆13Jan 26, 2026Updated last month
- Computational analyses of WGS, mate-pair, RNA-seq, Hi-C and Capture-C data from highly rearranged balancer chromosomes in Drosophila mela…☆10Sep 25, 2019Updated 6 years ago
- R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes☆21May 11, 2023Updated 2 years ago
- Hi-C data processing pipeline☆38Feb 27, 2024Updated 2 years ago
- Extract data quickly from Juicebox via straw☆69Apr 6, 2025Updated 10 months ago
- Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs☆11Dec 21, 2019Updated 6 years ago
- FIREcaller: an R package for detecting frequently interacting re-gions from Hi-C data☆12Nov 4, 2022Updated 3 years ago
- omics data analysis using clusterProfiler ;)☆15Jun 6, 2024Updated last year
- LoopPredictor: Predicting unknown enhancer-mediated genome topology by an ensemble machine learning model☆14Jun 18, 2021Updated 4 years ago
- Profile and Heatmap Visualization by Using ggplot2 and grid☆12Nov 21, 2023Updated 2 years ago
- General analysis of HiC data, including compartment A/B, domains and loops.☆14Feb 17, 2023Updated 3 years ago
- mouse_fullStack_annotations☆13Jun 29, 2023Updated 2 years ago
- ☆13Aug 9, 2024Updated last year
- Interspecies Point Projection - A tool for comparative genomics beyond alignable sequence☆23Feb 9, 2026Updated 3 weeks ago
- Extract 3D contacts (.pairs) from sequencing alignments☆125Feb 3, 2026Updated 3 weeks ago
- A Generalizable Model for 3D Chromosome Reconstruction Using Graph Convolutional Neural Networks☆18Sep 9, 2021Updated 4 years ago
- Tools for DLO HiC data analyze☆16Oct 31, 2022Updated 3 years ago
- Hi-C data super-resolution with generative adversarial networks☆15Jul 6, 2021Updated 4 years ago
- GENome Organisation Visual Analytics☆15Dec 24, 2021Updated 4 years ago
- A GAN-based method for Enhancing Hi-C data☆33Dec 17, 2020Updated 5 years ago
- An easy-to-use Hi-C data processing software supporting distributed computation.☆62Aug 6, 2024Updated last year
- ☆15Mar 12, 2021Updated 4 years ago
- A pipeline for identifying conserved topologically associating domain boundaries among multiple species.☆16Jun 17, 2025Updated 8 months ago
- SIP: Significant Interaction Peak caller☆15Apr 24, 2025Updated 10 months ago
- ☆23Jan 20, 2021Updated 5 years ago
- ☆16Dec 25, 2024Updated last year
- Genome-wide contact analysis using sklearn☆72Mar 23, 2024Updated last year
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆41Jan 31, 2024Updated 2 years ago
- R package to explore active transposable elements with RNA-seq data☆21Nov 25, 2022Updated 3 years ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆20Sep 12, 2023Updated 2 years ago
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 2 years ago
- Paired Insertion Counting for snATAC-seq data☆19May 12, 2025Updated 9 months ago
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 3 years ago
- ☆18Mar 12, 2024Updated last year
- Clustering TF motif models from multiple species (mostly focused on Drosophila and human) by similarity to remove redundancy☆29Dec 22, 2022Updated 3 years ago