Repositories list

• 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).

  HTML

  •

  GNU General Public License v3.0

  •0•5•0•0•Updated Aug 5, 2025Aug 5, 2025

• RoboATAC

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 2, 2025Aug 2, 2025

• array_analysis

  Public
  Snakemake pipeline for Greenleaf lab array preprocessing.

  Python

  •0•2•0•0•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

  •0•3•0•0•Updated Apr 28, 2025Apr 28, 2025

• BPCells_paper

  Public
  Benchmarking code & data from the BPCells 2025 paper

  R

  •

  MIT License

  •0•0•0•0•Updated Mar 27, 2025Mar 27, 2025

• amplicon-smf

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

  Python

  •

  MIT License

  •1•2•0•0•Updated Mar 24, 2025Mar 24, 2025

• shareseq-pipeline

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •2•7•0•0•Updated Mar 2, 2025Mar 2, 2025

• ArchR

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

  R

  •

  MIT License

  •149•425•155•15•Updated Feb 18, 2025Feb 18, 2025

• ArchR_Website

  Public
  CSS

  •4•0•0•0•Updated Feb 7, 2025Feb 7, 2025

• klf_manuscript_code

  Public
  Python

  •0•0•0•0•Updated Jan 28, 2025Jan 28, 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

  •69•0•0•0•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

  •0•0•0•0•Updated Sep 26, 2024Sep 26, 2024

• chromVAR

  Public
  chromatin Variability Across Regions (of the genome!)

  bioinformaticsdnase-seqr+ 1atac-seq

  R

  •

  Other

  •39•179•83•2•Updated Jul 10, 2024Jul 10, 2024

• snakeATAC_singularity

  Public
  Python

  •

  GNU General Public License v3.0

  •1•2•0•0•Updated Jun 5, 2024Jun 5, 2024

• motifmatchr

  Public
  Fast motif matching in R

  bioinformaticsrmotif-discovery

  C++

  •

  GNU General Public License v3.0

  •11•46•8•1•Updated Jan 24, 2024Jan 24, 2024

• scScalpChromatin

  Public
  R

  •12•27•0•0•Updated Sep 22, 2023Sep 22, 2023

• ChrAccR

  Public
  Analyzing chromatin accessibility data in R

  R

  •7•18•6•1•Updated Jun 23, 2023Jun 23, 2023

• NEAT-seq_reproducibility

  Public
  R

  •2•3•0•0•Updated Mar 4, 2022Mar 4, 2022

• brainchromatin

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

  R

  •7•33•1•0•Updated Jan 4, 2022Jan 4, 2022

• Brain_ASD

  Public
  Python

  •1•10•2•0•Updated Oct 4, 2021Oct 4, 2021

• TtAgo

  Public
  Python

  •0•0•0•0•Updated Sep 6, 2021Sep 6, 2021

• ArchR_2020

  Public
  Publication Page for ArchR Manuscript 2020

  HTML

  •9•22•2•0•Updated Aug 17, 2021Aug 17, 2021

• LKB1_2021

  Public
  R

  •

  MIT License

  •2•3•0•0•Updated Jun 27, 2021Jun 27, 2021

• SpearATAC_MS_2021

  Public
  R

  •

  MIT License

  •4•3•1•0•Updated Apr 1, 2021Apr 1, 2021

• array_fitting_tools

  Public
  Python

  •4•1•0•3•Updated Mar 9, 2021Mar 9, 2021

• matcha

  Public
  Python library for fast barcode matching in sequencing data

  Python

  •

  GNU General Public License v3.0

  •2•2•0•0•Updated Jan 3, 2021Jan 3, 2021

• NucleoATAC

  Public
  nucleosome calling using ATAC-seq

  bioinformaticsnuclesosomeatac-seq

  Python

  •

  MIT License

  •31•106•25•1•Updated Dec 20, 2020Dec 20, 2020

• MPAL-Single-Cell-2019

  Public
  Publication Page for MPAL Paper 2019

  R

  •38•83•16•1•Updated Jun 25, 2020Jun 25, 2020

• 10x-scATAC-2019

  Public
  Publication Page for Satpathy*, Granja* et al 2019

  R

  •55•95•11•1•Updated Apr 29, 2020Apr 29, 2020

• ChrAccRex

  Public
  Example data for ChrAccR

  R

  •0•1•0•0•Updated Jan 8, 2020Jan 8, 2020