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@3DGenomes

3DGenomes

Tools for modeling and analyzing 3D genomes.

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  1. TADbit TADbit Public

    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…

    Python 100 61

  2. TADdyn TADdyn Public

    TADdyn is a Python library that allows to model and explore single or time-series 3C-based data.

    Python 3

  3. TADpole TADpole Public

    TADpole is a computational tool designed to identify and analyze the entire hierarchy of topologically associated domains (TADs) in intra-chromosomal interaction matrices. This is the stable versio…

    R 9

  4. OligoFISSEQ OligoFISSEQ Public

    Example of the analysis workflow of one image produced by OligoFISSEQ. All the files needed are contained in this repository

    Jupyter Notebook 4 3

Repositories

Showing 10 of 19 repositories
  • METALoci Public

    METALoci: spatially auto-correlated signals in 3D genomes

    3DGenomes/METALoci’s past year of commit activity
    Python 2 GPL-3.0 0 0 0 Updated Oct 8, 2024
  • TADbit Public

    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 f…

    3DGenomes/TADbit’s past year of commit activity
    Python 100 GPL-3.0 61 66 1 Updated Jul 30, 2024
  • IMP_BioSystem_Domain_Fly_Genome Public

    Example of using IMP to model a region of the Fly genome https://integrativemodeling.org/systems/

    3DGenomes/IMP_BioSystem_Domain_Fly_Genome’s past year of commit activity
    Python 0 3 0 0 Updated Jun 21, 2023
  • Sox9_METALoci Public

    Code example of METALoci applied to H3K27ac for the Sox9 mouse locus during development (E13.5)

    3DGenomes/Sox9_METALoci’s past year of commit activity
    Jupyter Notebook 4 0 2 0 Updated Feb 9, 2023
  • TADkit Public archive

    3D Genome Browser

    3DGenomes/TADkit’s past year of commit activity
    JavaScript 31 MIT 10 31 (3 issues need help) 0 Updated Jan 22, 2022
  • OligoFISSEQ Public

    Example of the analysis workflow of one image produced by OligoFISSEQ. All the files needed are contained in this repository

    3DGenomes/OligoFISSEQ’s past year of commit activity
    Jupyter Notebook 4 3 0 0 Updated Jul 15, 2021
  • 3DAROC Public

    list of notebooks for 4 days course on Hi-C data handling and 3D modeling of chromatin

    3DGenomes/3DAROC’s past year of commit activity
    Jupyter Notebook 8 GPL-3.0 0 0 0 Updated Jul 2, 2021
  • SparseDataModelling Public Forked from julenmendieta/SparseDataModelling
    3DGenomes/SparseDataModelling’s past year of commit activity
    Jupyter Notebook 0 2 0 0 Updated Apr 9, 2021
  • loopbit Public

    Convolutional Neural Network to identify loops from 3C-based experiments

    3DGenomes/loopbit’s past year of commit activity
    Python 0 0 0 0 Updated Feb 27, 2021
  • TADdyn Public

    TADdyn is a Python library that allows to model and explore single or time-series 3C-based data.

    3DGenomes/TADdyn’s past year of commit activity
    Python 0 GPL-3.0 3 1 1 Updated Jan 27, 2021
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