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aryeelab

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  1. guideseq guideseq Public

    Analysis pipeline for the GUIDE-seq assay.

    Python 80 60

  2. hichipper hichipper Public

    A preprocessing and QC pipeline for HiChIP data

    HTML 40 15

  3. umi umi Public

    Preprocessing tools for unique molecular index (UMI) sequencing reads

    Python 31 27

  4. bisulfite-seq-tools bisulfite-seq-tools Public

    Suite of tools to conduct methylation data analysis. Methods from this workspace can be used for alignment and quality control analysis for various protocols including Whole Genom Bisulfite Sequenc…

    HTML 20 2

  5. colon-dna-topology colon-dna-topology Public

    Shell 5 2

  6. diffloop diffloop Public

    This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/diffloop.html Contributions: https://github.com/aryeelab/diffloop. …

    R 4 4

Repositories

Showing 10 of 61 repositories
  • topology-tools Public

    Processing pipelines for HiC and other 3D genome tools

    aryeelab/topology-tools’s past year of commit activity
    WDL 4 1 3 0 Updated Oct 3, 2025
  • aryeelab.dfci.harvard.edu Public Forked from caleblareau/steve-ngvb-jekyll-template

    Aryee Lab Webpage

    aryeelab/aryeelab.dfci.harvard.edu’s past year of commit activity
    JavaScript 0 MIT 101 0 0 Updated Oct 2, 2025
  • methyl-microc Public
    aryeelab/methyl-microc’s past year of commit activity
    Nextflow 0 MIT 0 0 0 Updated Sep 29, 2025
  • igv Public Forked from igvteam/igv

    Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

    aryeelab/igv’s past year of commit activity
    Java 0 MIT 400 0 0 Updated Jun 15, 2025
  • diffusion-walks Public
    aryeelab/diffusion-walks’s past year of commit activity
    Python 0 0 0 0 Updated Jun 10, 2025
  • cohesin_extrusion_reproducibility Public

    Code repository to reproduce all results for Sept, et al. 2023

    aryeelab/cohesin_extrusion_reproducibility’s past year of commit activity
    R 1 MIT 0 0 0 Updated Oct 14, 2024
  • nanopore-tools Public

    Tools for Oxford Nanopore

    aryeelab/nanopore-tools’s past year of commit activity
    WDL 2 1 3 0 Updated Aug 21, 2024
  • extrusion-sim Public
    aryeelab/extrusion-sim’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Feb 12, 2024
  • neochromatin Public
    aryeelab/neochromatin’s past year of commit activity
    R 1 0 0 0 Updated Nov 5, 2023
  • guideseq Public

    Analysis pipeline for the GUIDE-seq assay.

    aryeelab/guideseq’s past year of commit activity
    Python 80 AGPL-3.0 60 39 0 Updated Jun 14, 2023
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