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Search results for python hi c
hi-c
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32 search results found
Snakepipes
⭐
359
Customizable workflows based on snakemake and python for the analysis of NGS data
Hicexplorer
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197
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
Cooler
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183
A cool place to store your Hi-C
Cloops
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99
Accurate and flexible loops calling tool for 3D genomic data.
Tadbit
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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
Coolpuppy
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66
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
Pairix
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57
1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
Hic2cool
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50
Lightweight converter between hic and cool contact matrices.
Mustache
⭐
50
Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
C.origami
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47
C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
Chromosight
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46
Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
Hic_pipeline
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40
An easy-to-use Hi-C data processing software supporting distributed computation.
Hiclift
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39
A fast and efficient tool for converting chromatin interaction data between genome assemblies
Hicpeaks
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36
A Python implementation for BH-FDR and HiCCUPS
Polychrom
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35
Polymer simulations of chromosomes and generating "in silico" Hi-C maps
Clodius
⭐
33
Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.
Cloops2
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32
Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
Chess
⭐
24
Comparison of Hi-C Experiments using Structural Similarity.
Tadlib
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23
A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
Pgltools
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23
Paired Genomic Loci Tool Suite
Metator
⭐
20
Metagenomic binning based on Hi-C data
Quaich
⭐
19
snakemake pipeline for Hi-C post-processing
Higlass Server
⭐
17
Server component for HiGlass that manages and serves tiled data
Chromegcn
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16
Bioinformatics 2020: Graph Neural Networks for DNA Sequence Classification
Hicreppy
⭐
14
Python reimplementation of hicrep with compatibility for sparse matrices
Gcmapexplorer
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13
Genome Contact Map Explorer - gcMapExplorer. Visit:
Mhic
⭐
11
Pentad
⭐
9
A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.
3d Genome Builder
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8
3DGB is a workflow to build 3D models of genomes from HiC data
Viralcc
⭐
8
ViralCC: leveraging metagenomic proximity-ligation to retrieve complete viral genomes
Best Labs Of 3d Genome
⭐
8
Data and the co-authored network I extracted for lab selection in 3D genome research field
Hictools
⭐
6
Tools for processing HIC data.
Stripecaller
⭐
5
A toolkit for analyzing architectural stripes
Diffdomain
⭐
5
DiffDomain is a statistically sound method for detecting differential TADs between conditions
Pairsqc
⭐
5
QC report generator for Hi-C pairs file
Deephic
⭐
5
A GAN-based method for Enhancing Hi-C data
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