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GreenleafLab

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  1. ArchR ArchR Public

    ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

    R 390 139

  2. chromVAR chromVAR Public

    chromatin Variability Across Regions (of the genome!)

    R 161 38

  3. NucleoATAC NucleoATAC Public

    nucleosome calling using ATAC-seq

    Python 106 31

  4. 10x-scATAC-2019 10x-scATAC-2019 Public

    Publication Page for Satpathy*, Granja* et al 2019

    R 92 54

  5. MPAL-Single-Cell-2019 MPAL-Single-Cell-2019 Public

    Publication Page for MPAL Paper 2019

    R 77 39

  6. motifmatchr motifmatchr Public

    Fast motif matching in R

    C++ 43 11

Repositories

Showing 10 of 33 repositories
  • ABC-Enhancer-Gene-Prediction-CustomRegions Public Forked from broadinstitute/ABC-Enhancer-Gene-Prediction

    Adapted from original ABC repo to allow users to pass a custom set of candidate regions instead of built-in peak calling

    GreenleafLab/ABC-Enhancer-Gene-Prediction-CustomRegions’s past year of commit activity
    Python 0 MIT 64 0 0 Updated Nov 30, 2024
  • ArchR Public

    ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

    GreenleafLab/ArchR’s past year of commit activity
    R 390 MIT 139 132 (2 issues need help) 17 Updated Nov 28, 2024
  • nnn_paper Public

    Analysis for "High-Throughput DNA melt measurements enable improved models of DNA folding thermodynamics".

    GreenleafLab/nnn_paper’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Nov 18, 2024
  • array_analysis Public

    Snakemake pipeline for Greenleaf lab array preprocessing.

    GreenleafLab/array_analysis’s past year of commit activity
    Python 1 0 0 0 Updated Nov 18, 2024
  • synthetic_enhancer_footprinting_additional_materials Public

    Additional files for the analysis of Doughty*, Hinks*, Schaepe*, et al. Nature 2024.

    GreenleafLab/synthetic_enhancer_footprinting_additional_materials’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Sep 26, 2024
  • amplicon-smf Public

    Code for processing single-molecule footprinting data on synthetic amplicons (from Doughty*, Hinks*, Schaepe*, et al. 2024).

    GreenleafLab/amplicon-smf’s past year of commit activity
    Python 2 MIT 0 0 0 Updated Sep 25, 2024
  • chromVAR Public

    chromatin Variability Across Regions (of the genome!)

    GreenleafLab/chromVAR’s past year of commit activity
    R 161 38 77 2 Updated Jul 10, 2024
  • snakeATAC_singularity Public
    GreenleafLab/snakeATAC_singularity’s past year of commit activity
    Python 2 GPL-3.0 0 0 0 Updated Jun 5, 2024
  • shareseq-pipeline Public
    GreenleafLab/shareseq-pipeline’s past year of commit activity
    Python 5 AGPL-3.0 2 0 0 Updated May 3, 2024
  • motifmatchr Public

    Fast motif matching in R

    GreenleafLab/motifmatchr’s past year of commit activity
    C++ 43 GPL-3.0 11 7 1 Updated Jan 24, 2024
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