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  1. guideseq guideseq Public

    Analysis pipeline for the GUIDE-seq assay.

    Python 82 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 21 3

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

    Shell 6 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 69 repositories
  • methyl-microc Public
    aryeelab/methyl-microc's past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Jul 12, 2026
  • foci-3d Public
    aryeelab/foci-3d's past year of commit activity
    Jupyter Notebook 0 MIT 1 0 0 Updated Jun 9, 2026
  • no-hallucination-citations Public
    aryeelab/no-hallucination-citations's past year of commit activity
    0 0 0 0 Updated May 28, 2026
  • foci-3d-looping-factors Public
    aryeelab/foci-3d-looping-factors's past year of commit activity
    0 MIT 0 0 0 Updated Apr 26, 2026
  • 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 Apr 19, 2026
  • bwa Public Forked from lh3/bwa

    Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

    aryeelab/bwa's past year of commit activity
    C 0 GPL-3.0 587 0 0 Updated Apr 8, 2026
  • bioconda-recipes Public Forked from bioconda/bioconda-recipes

    Conda recipes for the bioconda channel.

    aryeelab/bioconda-recipes's past year of commit activity
    Shell 0 MIT 4,118 0 0 Updated Apr 5, 2026
  • 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 410 0 0 Updated Apr 4, 2026
  • codex-agent-project-skeleton Public
    aryeelab/codex-agent-project-skeleton's past year of commit activity
    0 0 0 0 Updated Apr 1, 2026
  • agent-skills Public
    aryeelab/agent-skills's past year of commit activity
    Python 0 0 0 0 Updated Mar 31, 2026
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