GreenleafLab

ArchR

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

chromVAR

chromatin Variability Across Regions (of the genome!)

NucleoATAC

nucleosome calling using ATAC-seq

10x-scATAC-2019

Publication Page for Satpathy*, Granja* et al 2019

MPAL-Single-Cell-2019

Publication Page for MPAL Paper 2019

motifmatchr

Fast motif matching in R

brainchromatin

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

NucleoATACR

R package for reading in & working with NucleoATAC outputs

ArchR_2020

Publication Page for ArchR Manuscript 2020

scScalpChromatin

ChrAccR

Analyzing chromatin accessibility data in R

Brain_ASD

shareseq-pipeline

LKB1_2021

NEAT-seq_reproducibility

SpearATAC_MS_2021

amplicon-smf

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

ImagingStationController

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

puflibs

snakeATAC_singularity

array_analysis

Snakemake pipeline for Greenleaf lab array preprocessing.

array_fitting_tools

ChrAccRex

Example data for ChrAccR

matcha

Python library for fast barcode matching in sequencing data

nnn_paper

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

ArchR_Website

TtAgo

ABC-Enhancer-Gene-Prediction-CustomRegions

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

lab-wiki

Repository to hold the lab wiki

synthetic_enhancer_footprinting_additional_materials

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