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GreenleafLab

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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

chromVARmotifs

R package with motifs for use with chromVAR

scScalpChromatin

ArchR_2020

Publication Page for ArchR Manuscript 2020

ChrAccR

Analyzing chromatin accessibility data in R

Brain_ASD

shareseq-pipeline

LKB1_2021

NEAT-seq_reproducibility

SpearATAC_MS_2021

ImagingStationController

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

puflibs

amplicon-smf

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

snakeATAC_singularity

array_fitting_tools

ChrAccRex

Example data for ChrAccR

nnn_paper

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

Jupyter Notebook

array_analysis

Snakemake pipeline for Greenleaf lab array preprocessing.

matcha

Python library for fast barcode matching in sequencing data