Repositories list

• amplicon-smf

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

  Python

  •

  MIT License

  •22 forks•77 stars•00 issues•11 pull request•Updated Sep 4, 2026Sep 4, 2026

• HDMA

  Public
  Code & documentation for Multiomics and deep learning dissect regulatory syntax in human development (Liu*, Jessa*, Kim*, Ng*, et al, Nature, 2026).

  HTML

  •

  GNU General Public License v3.0

  •22 forks•3030 stars•00 issues•00 pull requests•Updated Jul 17, 2026Jul 17, 2026

• PIP-ATAC-Pipeline

  Public
  Testing pipeline for PIP-ATAC-seq

  Python

  •00 forks•22 stars•00 issues•00 pull requests•Updated May 29, 2026May 29, 2026

• shareseq-pipeline

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •22 forks•99 stars•00 issues•00 pull requests•Updated May 19, 2026May 19, 2026

• BPCells

  Public
  BPCells GreenleafLab Fork

  C++

  •

  Other

  •3737 forks•00 stars•00 issues•00 pull requests•Updated May 7, 2026May 7, 2026

• chromVAR

  Public
  chromatin Variability Across Regions (of the genome!)

  bioinformaticsdnase-seqr+ 1

  bioinformaticsdnase-seqratac-seq

  R

  •

  Other

  •4040 forks•196196 stars•8484 issues•33 pull requests•Updated May 1, 2026May 1, 2026

• klf_manuscript_code

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 2, 2025Oct 2, 2025

• HLDA

  Public
  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 26, 2025Sep 26, 2025

• ArchR_Website

  Public
  CSS

  •44 forks•00 stars•00 issues•00 pull requests•Updated Sep 25, 2025Sep 25, 2025

• RoboATAC

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Aug 2, 2025Aug 2, 2025

• array_analysis

  Public
  Snakemake pipeline for Greenleaf lab array preprocessing.

  Python

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 1, 2025Jul 1, 2025

• nnn_paper

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

  Jupyter Notebook

  •

  MIT License

  •11 fork•66 stars•22 issues•00 pull requests•Updated Apr 28, 2025Apr 28, 2025

• BPCells_paper

  Public
  Benchmarking code & data from the BPCells 2025 paper

  R

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 27, 2025Mar 27, 2025

• ArchR

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

  R

  •

  MIT License

  •159159 forks•465465 stars•164164 issues•1717 pull requests•Updated Feb 18, 2025Feb 18, 2025

• ABC-Enhancer-Gene-Prediction-CustomRegions

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

  Python

  •

  MIT License

  •7878 forks•11 star•00 issues•00 pull requests•Updated Nov 30, 2024Nov 30, 2024

• synthetic_enhancer_footprinting_additional_materials

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

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 26, 2024Sep 26, 2024

• snakeATAC_singularity

  Public
  Python

  •

  GNU General Public License v3.0

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jun 5, 2024Jun 5, 2024

• motifmatchr

  Public
  Fast motif matching in R

  bioinformaticsrmotif-discovery

  bioinformaticsrmotif-discovery

  C++

  •

  GNU General Public License v3.0

  •1313 forks•4949 stars•88 issues•22 pull requests•Updated Jan 24, 2024Jan 24, 2024

• scScalpChromatin

  Public
  R

  •1414 forks•3131 stars•00 issues•00 pull requests•Updated Sep 22, 2023Sep 22, 2023

• NEAT-seq_reproducibility

  Public
  R

  •33 forks•33 stars•00 issues•00 pull requests•Updated Mar 4, 2022Mar 4, 2022

• brainchromatin

  Public
  Code used to analyze single cell RNA and ATAC sequencing in developing human brain

  R

  •77 forks•3636 stars•11 issue•00 pull requests•Updated Jan 4, 2022Jan 4, 2022

• Brain_ASD

  Public
  Python

  •22 forks•1212 stars•22 issues•00 pull requests•Updated Oct 4, 2021Oct 4, 2021

• TtAgo

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 6, 2021Sep 6, 2021

• ArchR_2020

  Public
  Publication Page for ArchR Manuscript 2020

  HTML

  •1010 forks•2424 stars•22 issues•00 pull requests•Updated Aug 17, 2021Aug 17, 2021

• LKB1_2021

  Public
  R

  •

  MIT License

  •33 forks•33 stars•00 issues•00 pull requests•Updated Jun 27, 2021Jun 27, 2021

• SpearATAC_MS_2021

  Public
  R

  •

  MIT License

  •44 forks•33 stars•11 issue•00 pull requests•Updated Apr 1, 2021Apr 1, 2021

• array_fitting_tools

  Public
  Python

  •44 forks•11 star•00 issues•33 pull requests•Updated Mar 9, 2021Mar 9, 2021

• matcha

  Public
  Python library for fast barcode matching in sequencing data

  Python

  •

  GNU General Public License v3.0

  •22 forks•22 stars•00 issues•00 pull requests•Updated Jan 3, 2021Jan 3, 2021

• NucleoATAC

  Public
  nucleosome calling using ATAC-seq

  bioinformaticsatac-seqnuclesosome

  bioinformaticsatac-seqnuclesosome

  Python

  •

  MIT License

  •3434 forks•113113 stars•2525 issues•22 pull requests•Updated Dec 20, 2020Dec 20, 2020

• MPAL-Single-Cell-2019

  Public
  Publication Page for MPAL Paper 2019

  R

  •3939 forks•8686 stars•1616 issues•11 pull request•Updated Jun 25, 2020Jun 25, 2020