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GreenleafLab

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  1. ArchR ArchR Public

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

    R 442 152

  2. chromVAR chromVAR Public

    chromatin Variability Across Regions (of the genome!)

    R 185 39

  3. NucleoATAC NucleoATAC Public

    nucleosome calling using ATAC-seq

    Python 109 32

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

    Publication Page for Satpathy*, Granja* et al 2019

    R 95 56

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

    Publication Page for MPAL Paper 2019

    R 83 39

  6. motifmatchr motifmatchr Public

    Fast motif matching in R

    C++ 46 11

Repositories

Showing 10 of 38 repositories
  • 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 3 MIT 2 0 1 Updated Dec 11, 2025
  • HDMA Public

    Code & documentation for Dissecting regulatory syntax in human development with scalable multiomics and deep learning (Liu*, Jessa*, Kim*, Ng*, et al, bioRxiv, 2025).

    GreenleafLab/HDMA’s past year of commit activity
    HTML 9 GPL-3.0 0 0 0 Updated Dec 7, 2025
  • shareseq-pipeline Public
    GreenleafLab/shareseq-pipeline’s past year of commit activity
    Python 7 AGPL-3.0 2 0 0 Updated Dec 7, 2025
  • klf_manuscript_code Public
    GreenleafLab/klf_manuscript_code’s past year of commit activity
    Python 0 0 0 0 Updated Oct 2, 2025
  • HLDA Public
    GreenleafLab/HLDA’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Sep 26, 2025
  • ArchR_Website Public
    GreenleafLab/ArchR_Website’s past year of commit activity
    CSS 0 4 0 0 Updated Sep 25, 2025
  • RoboATAC Public
    GreenleafLab/RoboATAC’s past year of commit activity
    Jupyter Notebook 1 GPL-3.0 0 1 0 Updated Aug 2, 2025
  • array_analysis Public

    Snakemake pipeline for Greenleaf lab array preprocessing.

    GreenleafLab/array_analysis’s past year of commit activity
    Python 2 0 0 0 Updated Jul 1, 2025
  • 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 4 MIT 0 0 0 Updated Apr 28, 2025
  • BPCells_paper Public

    Benchmarking code & data from the BPCells 2025 paper

    GreenleafLab/BPCells_paper’s past year of commit activity
    R 1 MIT 0 0 0 Updated Mar 27, 2025
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