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The Top 23 Python Hi C Open Source Projects

Open source projects categorized as Python Hi C
Snakepipes ⭐ 359
Customizable workflows based on snakemake and python for the analysis of NGS data
most recent commit 3 months ago
Hicexplorer ⭐ 197
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
most recent commit 5 months ago
Cooler ⭐ 183
A cool place to store your Hi-C
dependent packages 27total releases 45most recent commit 3 months agopypi cooler} Downloads
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 a year ago
Coolpuppy ⭐ 66
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
total releases 23most recent commit 3 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
Hic2cool ⭐ 50
Lightweight converter between hic and cool contact matrices.
dependent packages 1total releases 29most recent commit 5 months agopypi hic2cool} 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 8 months ago
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
Hic_pipeline ⭐ 40
An easy-to-use Hi-C data processing software supporting distributed computation.
total releases 60most recent commit a year ago
Hiclift ⭐ 39
A fast and efficient tool for converting chromatin interaction data between genome assemblies
total releases 8most recent commit 10 months ago
Hicpeaks ⭐ 36
A Python implementation for BH-FDR and HiCCUPS
total releases 14most recent commit 8 months ago
Polychrom ⭐ 35
Polymer simulations of chromosomes and generating "in silico" Hi-C maps
most recent commit 8 months ago
Clodius ⭐ 33
Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.
dependent packages 3total releases 90most recent commit a year agopypi clodius} Downloads
Cloops2 ⭐ 32
Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
total releases 6most recent commit 6 months ago
Chess ⭐ 24
Comparison of Hi-C Experiments using Structural Similarity.
total releases 10most recent commit 9 months ago
Tadlib ⭐ 23
A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
total releases 31most recent commit 2 years ago
Pgltools ⭐ 23
Paired Genomic Loci Tool Suite
total releases 13most recent commit a year ago
Metator ⭐ 20
Metagenomic binning based on Hi-C data
total releases 17most recent commit 3 months ago
Quaich ⭐ 19
snakemake pipeline for Hi-C post-processing
most recent commit 4 months ago
Higlass Server ⭐ 17
Server component for HiGlass that manages and serves tiled data
most recent commit 2 years ago
The 5 Most Depended On Python Hi C Open Source Projects
Cooler ⭐ 183
A cool place to store your Hi-C
dependent packages 27total releases 45latest release September 11, 2023most recent commit 3 months 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
Hic2cool ⭐ 50
Lightweight converter between hic and cool contact matrices.
dependent packages 1total releases 29latest release November 14, 2023most recent commit 5 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 Python Hi C Open Source Projects
Hic2cool ⭐ 50
Lightweight converter between hic and cool contact matrices.
dependent packages 1total releases 29latest release November 14, 2023most recent commit 5 months agopypi hic2cool} Downloads
Cooler ⭐ 183
A cool place to store your Hi-C
dependent packages 27total releases 45latest release September 11, 2023most recent commit 3 months agopypi cooler} 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 8 months ago
Hicpeaks ⭐ 36
A Python implementation for BH-FDR and HiCCUPS
total releases 14latest release August 14, 2023most recent commit 8 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 6 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 3 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
C.origami ⭐ 47
C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
total releases 1latest release November 28, 2022most recent commit 4 months ago
Hiclift ⭐ 39
A fast and efficient tool for converting chromatin interaction data between genome assemblies
total releases 8latest release October 13, 2022most recent commit 10 months ago
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