DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data
☆35Apr 1, 2025Updated last year
Alternatives and similar repositories for DeepLoop
Users that are interested in DeepLoop are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- HiCorr: a Hi-C data bias-correction pipeline☆30Apr 1, 2025Updated last year
- Web-Application for the cross-visualization of HiC and ChIP-seq data.☆18Feb 17, 2026Updated last month
- Super-resolution chromatin tracing 2018☆18Nov 7, 2020Updated 5 years ago
- R package to evaluate reproducibility of Hi-C data☆10Mar 16, 2023Updated 3 years ago
- An Optimized Nested TAD caller for Hi-C data☆25Jun 30, 2021Updated 4 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆42Jan 31, 2024Updated 2 years ago
- R package to evaluate the reproducibility of Hi-C data☆27Jun 23, 2023Updated 2 years ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆20Sep 12, 2023Updated 2 years ago
- Genome-wide contact analysis using sklearn☆74Mar 23, 2024Updated 2 years ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆92Oct 29, 2025Updated 5 months ago
- Poisson-based algorithm for stable inference of DNA Structure☆39Updated this week
- iFISH Probe Design: a Python3 package to build iFISH probes.☆12Mar 11, 2022Updated 4 years ago
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 3 years ago
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 3 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.☆53Jun 17, 2025Updated 9 months ago
- A 3D genome data processing tutorial for ISMB/ECCB 2017☆52Jul 21, 2017Updated 8 years ago
- ☆16Jul 21, 2022Updated 3 years ago
- Scripts + resources for analyzing combinatorial Hi-C data☆32Nov 5, 2019Updated 6 years ago
- The tools for your .cool's☆163Mar 19, 2026Updated 3 weeks ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment☆21Apr 8, 2024Updated 2 years ago
- code associated with crane-nature-2015, 10.1038/nature14450☆36Aug 28, 2015Updated 10 years ago
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆84Mar 22, 2026Updated 2 weeks ago
- An easy-to-use Hi-C data processing software supporting distributed computation.☆62Aug 6, 2024Updated last year
- Wordpress hosting with auto-scaling on Cloudways • AdFully Managed hosting built for WordPress-powered businesses that need reliable, auto-scalable hosting. Cloudways SafeUpdates now available.
- Package Homepage: http://bioconductor.org/packages/devel/bioc/html/DRIMSeq.html Bug Reports: https://support.bioconductor.org/p/new/post/…☆12Aug 5, 2020Updated 5 years ago
- Simple library/pipeline to generate and handle Hi-C data.☆39Feb 13, 2026Updated last month
- Tools for DLO HiC data analyze☆16Oct 31, 2022Updated 3 years ago
- ☆16Updated this week
- Cluster-based analysis of CpG methylation☆13Jan 11, 2024Updated 2 years ago
- Lightweight converter between hic and cool contact matrices.☆74Jul 15, 2024Updated last year
- Python bindings for hictk: read and write .cool and .hic files directly from Python☆16Mar 30, 2026Updated last week
- Software to compute reproducibility and quality scores for Hi-C data☆50Apr 12, 2019Updated 6 years ago
- Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020☆21Jul 13, 2023Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆97Mar 1, 2025Updated last year
- Tools to analyze Dip-C (or other 3C/Hi-C) data☆75Mar 28, 2026Updated last week
- Notes on single-cell Hi-C technologies, tools, and data☆88Feb 28, 2026Updated last month
- Python package to predict enhancer-gene interactions supervised on CRISPRi data☆15Nov 21, 2023Updated 2 years ago
- Scripts used for the ACT paper☆12May 6, 2021Updated 4 years ago
- a computational tool for analyzing single cell Hi-C data☆26Apr 23, 2024Updated last year
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 2 years ago