SIP: Significant Interaction Peak caller
☆16Apr 24, 2025Updated 10 months ago
Alternatives and similar repositories for SIP
Users that are interested in SIP 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
- Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps☆70Dec 16, 2022Updated 3 years ago
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years ago
- 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
- Software to compute reproducibility and quality scores for Hi-C data☆50Apr 12, 2019Updated 6 years ago
- The tools for your .cool's☆161Jul 7, 2025Updated 8 months ago
- GENome Organisation Visual Analytics☆86Feb 3, 2026Updated last month
- SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.☆17Jun 1, 2023Updated 2 years ago
- Genome-wide contact analysis using sklearn☆74Mar 23, 2024Updated last year
- code associated with crane-nature-2015, 10.1038/nature14450☆36Aug 28, 2015Updated 10 years ago
- A toolkit for analyzing architectural stripes☆20Dec 1, 2024Updated last year
- Hi-C Interaction Frequency Inference (HIFI): High-resolution estimation of DNA-DNA interaction frequency from Hi-C data☆24Sep 28, 2022Updated 3 years ago
- HiCnv is used to call copy number variations and breakpoints from Hi-C data☆23Mar 30, 2024Updated last year
- FAN-C: Framework for the ANalysis of C-like data☆122Mar 13, 2024Updated 2 years ago
- Comparison of Hi-C Experiments using Structural Similarity.☆28Jul 18, 2023Updated 2 years ago
- 1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates☆92Jan 28, 2025Updated last year
- Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation☆80Jan 24, 2025Updated last year
- GENome Organisation Visual Analytics☆15Dec 24, 2021Updated 4 years ago
- Reference-free quality assessment for Hi-C sequencing data☆13Apr 30, 2024Updated last year
- Docker for 4DN Hi-C processing pipeline☆61Nov 26, 2024Updated last year
- Joint normalization of multiple Hi-C matrices, visualization and detection of differential chromatin interactions, supporting covariates.☆10Apr 22, 2022Updated 3 years ago
- Hi-C data analysis tool☆13May 31, 2017Updated 8 years ago
- R package to evaluate the reproducibility of Hi-C data☆27Jun 23, 2023Updated 2 years ago
- Red-C data processing☆15Apr 18, 2023Updated 2 years ago
- A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.☆14Mar 9, 2023Updated 3 years ago
- A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains☆45Aug 4, 2022Updated 3 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
- An Optimized Nested TAD caller for Hi-C data☆25Jun 30, 2021Updated 4 years ago
- Genome Contact Map Explorer - gcMapExplorer. Visit:☆21Jan 23, 2022Updated 4 years ago
- dcHiC: Differential compartment analysis for Hi-C datasets☆74Jan 10, 2024Updated 2 years ago
- A machine-learning algorithm to predict CTCF-mediated long-range chromatin interactions☆17Nov 7, 2018Updated 7 years ago
- A versatile tool to perform pile-up analysis on Hi-C data in .cool format.☆81Oct 31, 2024Updated last year
- High-performance stochastic modeling of DNA loop extrusion interactions☆18Dec 22, 2025Updated 2 months ago
- ☆18Nov 9, 2020Updated 5 years ago
- snakemake pipeline for Hi-C post-processing☆22Jun 27, 2024Updated last year
- Blazing fast toolkit to work with .hic and .cool files☆42Mar 9, 2026Updated last week
- RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.☆41Feb 14, 2022Updated 4 years ago
- A Python implementation of the original DI domain caller☆12Aug 2, 2020Updated 5 years ago
- STARRPeaker: STARR-seq peak caller☆17Jul 6, 2022Updated 3 years ago