High-performance stochastic modeling of DNA loop extrusion interactions
☆18Dec 22, 2025Updated 3 months ago
Alternatives and similar repositories for modle
Users that are interested in modle are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Blazing fast toolkit to work with .hic and .cool files☆42Mar 16, 2026Updated last week
- A toolkit for analyzing architectural stripes☆20Dec 1, 2024Updated last year
- 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 3 months 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
- 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
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years ago
- A pipeline for identifying conserved topologically associating domain boundaries among multiple species.☆16Jun 17, 2025Updated 9 months ago
- dcHiC: Differential compartment analysis for Hi-C datasets☆74Jan 10, 2024Updated 2 years ago
- Architectural stripe detection from 3D genome conformation data☆18Sep 15, 2025Updated 6 months ago
- 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs☆13Oct 15, 2025Updated 5 months ago
- Interspecies Point Projection - A tool for comparative genomics beyond alignable sequence☆25Feb 9, 2026Updated last month
- Python bindings to UCSC BigWig and BigBed library☆36Mar 13, 2026Updated last week
- Plotting average TAD heatmap for Hi-C data (give TAD segmentation and cool/hiclib interactions map).☆10Jun 5, 2021Updated 4 years ago
- Python bindings for hictk: read and write .cool and .hic files directly from Python☆16Mar 16, 2026Updated last week
- 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.
- Transposable element expression at unique loci in single cells with CELLO-seq☆11Jun 17, 2024Updated last year
- omics data analysis using clusterProfiler ;)☆15Jun 6, 2024Updated last year
- 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
- snakemake pipeline for Hi-C post-processing☆22Jun 27, 2024Updated last year
- ☆12Jun 7, 2024Updated last year
- QC report generator for Hi-C pairs file☆13Sep 14, 2020Updated 5 years ago
- HiCDCPlus☆19Jun 6, 2022Updated 3 years ago
- Implementation of the AIControl paper in Julia 1.0☆17Mar 4, 2019Updated 7 years ago
- A Python implementation of the original DI domain caller☆12Aug 2, 2020Updated 5 years ago
- 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.
- Red-C data processing☆15Apr 18, 2023Updated 2 years ago
- Chromatin States Map in mouse embryonic stem cell☆19Apr 11, 2018Updated 7 years ago
- SIP: Significant Interaction Peak caller☆16Apr 24, 2025Updated 11 months ago
- Chromosome polymer simulations and in silico capture experiments☆56Feb 18, 2026Updated last month
- ☆16Mar 16, 2017Updated 9 years ago
- ☆12Nov 20, 2023Updated 2 years ago
- gghic makes visualization of Hi-C/-like data easily in R☆26Jan 23, 2026Updated 2 months ago
- code associated with crane-nature-2015, 10.1038/nature14450☆36Aug 28, 2015Updated 10 years ago
- Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.☆53Jun 17, 2025Updated 9 months 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.
- Explore the Hi-Cs☆11Nov 30, 2025Updated 3 months ago
- HiC uniform processing pipeline☆63Nov 8, 2023Updated 2 years ago
- perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)☆67Jun 7, 2019Updated 6 years ago
- Genome-wide contact analysis using sklearn☆74Mar 23, 2024Updated 2 years ago
- DiffDomain is a statistically sound method for detecting differential TADs between conditions☆17Jun 27, 2025Updated 8 months ago
- A Jupyter wrapper for the igv.js library (representation of genomic data)☆26Feb 16, 2021Updated 5 years ago
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆80Jan 24, 2025Updated last year