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The Top 23 Hi C Open Source Projects

Open source projects categorized as Hi C
Categories > Hi C
Hic_tools ⭐ 454
A collection of tools for Hi-C data analysis
most recent commit 5 months ago
Snakepipes ⭐ 359
Customizable workflows based on snakemake and python for the analysis of NGS data
most recent commit 4 months ago
Juicer ⭐ 313
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
most recent commit a year ago
Higlass ⭐ 300
Fast, flexible and extensible genome browser.
dependent packages 43total releases 240most recent commit 3 months agonpm higlass} Downloads
Hicexplorer ⭐ 197
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
most recent commit 6 months ago
Cooler ⭐ 191
A cool place to store your Hi-C
dependent packages 27total releases 45most recent commit 7 days agopypi cooler} Downloads
Salsa ⭐ 153
SALSA: A tool to scaffold long read assemblies with Hi-C data
most recent commit 2 years ago
Hic_data ⭐ 128
A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
most recent commit 7 months ago
Cloops ⭐ 99
Accurate and flexible loops calling tool for 3D genomic data.
most recent commit 2 years ago
Tadbit ⭐ 89
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 FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
most recent commit 2 years ago
Distiller Nf ⭐ 80
A modular Hi-C mapping pipeline
most recent commit 5 months ago
Hic Data Analysis Bootcamp ⭐ 78
Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
most recent commit 6 years ago
Hickit ⭐ 69
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
most recent commit 3 years ago
Coolpuppy ⭐ 66
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
total releases 23most recent commit 4 months ago
Hic ⭐ 63
Analysis of Chromosome Conformation Capture data (Hi-C)
most recent commit 6 months ago
Pairix ⭐ 57
1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
dependent packages 5total releases 34most recent commit 3 years agopypi pypairix} Downloads
Mustache ⭐ 50
Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
total releases 48most recent commit 9 months ago
Hic2cool ⭐ 50
Lightweight converter between hic and cool contact matrices.
dependent packages 1total releases 29most recent commit 6 months agopypi hic2cool} Downloads
C.origami ⭐ 47
C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
total releases 1most recent commit 4 months ago
Chromosight ⭐ 46
Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
dependent packages 1total releases 55most recent commit a year agopypi chromosight} Downloads
Dchic ⭐ 44
dcHiC: Differential compartment analysis for Hi-C datasets
most recent commit 4 months ago
Genova ⭐ 43
GENome Organisation Visual Analytics
most recent commit a year ago
Allhic ⭐ 41
Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
total releases 8most recent commit 3 years ago
The 7 Most Depended On Hi C Open Source Projects
Higlass ⭐ 300
Fast, flexible and extensible genome browser.
dependent packages 43total releases 240latest release November 28, 2023most recent commit 3 months agonpm higlass} Downloads
Cooler ⭐ 191
A cool place to store your Hi-C
dependent packages 27total releases 45latest release September 11, 2023most recent commit 7 days agopypi cooler} Downloads
Pairix ⭐ 57
1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
dependent packages 5total releases 34latest release April 11, 2019most recent commit 3 years agopypi pypairix} Downloads
Hicstuff ⭐ 17
Simple library/pipeline to generate and handle Hi-C data.
dependent packages 1total releases 128latest release September 06, 2023most recent commit 3 years agopypi hicstuff} Downloads
Hic2cool ⭐ 50
Lightweight converter between hic and cool contact matrices.
dependent packages 1total releases 29latest release November 14, 2023most recent commit 6 months agopypi hic2cool} Downloads
Chromosight ⭐ 46
Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
dependent packages 1total releases 55latest release October 05, 2022most recent commit a year agopypi chromosight} Downloads
The 10 Latest Releases In Hi C Open Source Projects
Higlass ⭐ 300
Fast, flexible and extensible genome browser.
dependent packages 43total releases 240latest release November 28, 2023most recent commit 3 months agonpm higlass} Downloads
Hic2cool ⭐ 50
Lightweight converter between hic and cool contact matrices.
dependent packages 1total releases 29latest release November 14, 2023most recent commit 6 months agopypi hic2cool} Downloads
Cooler ⭐ 191
A cool place to store your Hi-C
dependent packages 27total releases 45latest release September 11, 2023most recent commit 7 days agopypi cooler} Downloads
Hicstuff ⭐ 17
Simple library/pipeline to generate and handle Hi-C data.
dependent packages 1total releases 128latest release September 06, 2023most recent commit 3 years agopypi hicstuff} Downloads
Mustache ⭐ 50
Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
total releases 48latest release August 29, 2023most recent commit 9 months ago
Hicpeaks ⭐ 36
A Python implementation for BH-FDR and HiCCUPS
total releases 14latest release August 14, 2023most recent commit 9 months ago
Cloops2 ⭐ 32
Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
total releases 6latest release July 20, 2023most recent commit 7 months ago
Coolpuppy ⭐ 66
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
total releases 23latest release July 11, 2023most recent commit 4 months ago
Hic_pipeline ⭐ 40
An easy-to-use Hi-C data processing software supporting distributed computation.
total releases 60latest release January 19, 2023most recent commit a year ago
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