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@koszullab Romain Koszul Laboratory

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    18 repositories

    • hicstuff

      Public
      Simple library/pipeline to generate and handle Hi-C data.
      bioinformaticsgenomicsbioinformatics-pipelinehi-c3c
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•37•6•0•Updated May 30, 2024May 30, 2024

    • metaTOR

      Public
      Metagenomic binning based on Hi-C data
      metagenomicshi-c3cmetagenome-assemblylouvain-community-detectionmetagenomic-pipeline
      Python
      •
      GNU General Public License v3.0
      •10•24•0•0•Updated Mar 27, 2024Mar 27, 2024

    • instaGRAAL

      Public
      Large genome reassembly based on Hi-C data, continuation of GRAAL
      genomicshi-cscaffolding3cgenome-assembly
      Cuda
      •
      GNU General Public License v3.0
      •9•40•7•0•Updated Mar 20, 2024Mar 20, 2024

    • HiContacts

      Public
      HiContacts: R interface to cool files and analysis of Hi-C contacts
      R
      •
      Other
      •1•1•0•0•Updated Jan 27, 2024Jan 27, 2024

    • chromosight_analyses_scripts

      Public
      Codes used to perform analyses in the Chromosight publication
      Python
      •0•4•0•0•Updated Nov 17, 2023Nov 17, 2023

    • transcription_T7_analysis

      Public
      In this repository, we present the code for the analysis of study of the transcription's impact on Escherichia coli chromosome.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Oct 1, 2023Oct 1, 2023

    • bacchus

      Public
      Tools for analysis of BACterial Chromosome HiC data. (BACCHUS)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Sep 4, 2023Sep 4, 2023

    • chromosight

      Public
      Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
      genomicshi-cpattern-detectionchromatin-loops
      Python
      •
      Other
      •9•62•4•0•Updated Dec 16, 2022Dec 16, 2022

    • GRAAL

      Public
      (check out instaGRAAL for a faster, updated program!) This program is from Marie-Nelly et al., Nature Communications, 2014 (High-quality genome assembly using chromosomal contact data), also Marie-Nelly et al., 2013, PhD thesis (https://www.theses.fr/2013PA066714)
      Python
      •9•14•8•4•Updated Nov 22, 2022Nov 22, 2022

    • serpentine

      Public
      Local, normalization-free contact map binning
      hi-c3c
      Python
      •
      Other
      •3•5•0•1•Updated Oct 24, 2022Oct 24, 2022

    • HiC_reassembler

      Public
      Python
      •2•0•0•0•Updated Aug 31, 2022Aug 31, 2022

    • pareidolia

      Public
      Multi-sample change detection in Hi-C patterns
      genomicshi-cchange-detection
      Python
      •
      MIT License
      •3•9•1•0•Updated Feb 25, 2022Feb 25, 2022

    • E_coli_analysis

      Public
      Relates to the article by Lioy, Cournac et al., Cell, 2018 (Functional partitioning of a bacterial chromosome through the interplay of nucleoid- associated proteins and the condensin MukBEF)
      Python
      •3•11•0•0•Updated Aug 19, 2020Aug 19, 2020

    • ectocarpus_scripts

      Public
      Scripts and materials needed to reproduce results and figures in the instaGRAAL showcase paper
      Python
      •1•3•0•0•Updated Apr 16, 2020Apr 16, 2020

    • 3C_tutorial

      Public
      Step by step command-line tutorial to process Hi-C data
      hi-c3c
      Python
      •9•4•0•0•Updated Jan 14, 2020Jan 14, 2020

    • HiC-Box

      Public
      GUI-based pipeline for Hi-C data processing and visualization
      Python
      •6•5•2•0•Updated Apr 2, 2019Apr 2, 2019

    • centroID

      Public
      Identification of centromere from chromosomal contact maps Marie-Nelly, Marbouty et al., Bioinformatics, 2014
      Python
      •1•2•0•0•Updated Nov 20, 2018Nov 20, 2018

    • DADE

      Public
      Perl
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 19, 2017Dec 19, 2017