Repositories list

• ArchR

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

  R

  •

  MIT License

  •139•387•133•16•Updated Nov 14, 2024Nov 14, 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

• amplicon-smf

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

  Python

  •

  MIT License

  •0•2•0•0•Updated Sep 25, 2024Sep 25, 2024

• chromVAR

  Public
  chromatin Variability Across Regions (of the genome!)

  bioinformaticsdnase-seqr+ 1atac-seq

  R

  •

  Other

  •38•159•76•2•Updated Jul 10, 2024Jul 10, 2024

• snakeATAC_singularity

  Public
  Python

  •

  GNU General Public License v3.0

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

• shareseq-pipeline

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •2•5•0•0•Updated May 3, 2024May 3, 2024

• motifmatchr

  Public
  Fast motif matching in R

  bioinformaticsrmotif-discovery

  C++

  •

  GNU General Public License v3.0

  •11•43•7•1•Updated Jan 24, 2024Jan 24, 2024

• array_analysis

  Public
  Snakemake pipeline for Greenleaf lab array preprocessing.

  Python

  •0•1•0•0•Updated Jan 19, 2024Jan 19, 2024

• nnn_paper

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

  Jupyter Notebook

  •0•1•0•0•Updated Jan 19, 2024Jan 19, 2024

• scScalpChromatin

  Public
  R

  •11•22•1•0•Updated Sep 22, 2023Sep 22, 2023

• ChrAccR

  Public
  Analyzing chromatin accessibility data in R

  R

  •7•18•5•1•Updated Jun 23, 2023Jun 23, 2023

• ArchR_Website

  Public
  CSS

  •3•0•0•0•Updated Feb 27, 2023Feb 27, 2023

• NEAT-seq_reproducibility

  Public
  R

  •2•3•1•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•31•2•0•Updated Jan 4, 2022Jan 4, 2022

• Brain_ASD

  Public
  Python

  •1•9•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

  •1•1•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•77•16•1•Updated Jun 25, 2020Jun 25, 2020

• 10x-scATAC-2019

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

  R

  •54•92•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

• lab-wiki

  Public
  Repository to hold the lab wiki

  0•0•0•0•Updated Jan 22, 2019Jan 22, 2019

• puflibs

  Public
  Python

  •0•2•0•0•Updated Jan 21, 2019Jan 21, 2019

• NucleoATACR

  Public
  R package for reading in & working with NucleoATAC outputs

  R

  •

  Other

  •12•26•0•0•Updated Oct 13, 2018Oct 13, 2018

• ImagingStationController

  Public
  Hardware-control software for a sequencing flowcell imaging station based on GAIIx components

  MATLAB

  •

  Apache License 2.0

  •1•2•0•0•Updated Jul 5, 2018Jul 5, 2018

• basic_data_exploration

  Public archive
  Python

  •0•0•0•0•Updated May 3, 2018May 3, 2018