GreenleafLab

Pinned Repositories

10x-scATAC-2019
Publication Page for Satpathy*, Granja* et al 2019
Language:R92 9 1654
ArchR
ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
Language:R390 15 1.1k140
ArchR_2020
Publication Page for ArchR Manuscript 2020
Language:HTML22 9 139
brainchromatin
Code used to analyze single cell RNA and ATAC sequencing in developing human brain
Language:R31 4 167
chromVAR
chromatin Variability Across Regions (of the genome!)
Language:R162 21 11238
chromVARmotifs
R package with motifs for use with chromVAR
Language:R25 13 89
motifmatchr
Fast motif matching in R
Language:C++43 11 911
MPAL-Single-Cell-2019
Publication Page for MPAL Paper 2019
Language:R77 13 2538
NucleoATAC
nucleosome calling using ATAC-seq
Language:Python106 19 9231
NucleoATACR
R package for reading in & working with NucleoATAC outputs
Language:R26 10 212

GreenleafLab's Repositories

GreenleafLab/ArchR
ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
Language:R390 15 1.1k140
GreenleafLab/chromVAR
chromatin Variability Across Regions (of the genome!)
Language:R162 21 11238
GreenleafLab/NucleoATAC
nucleosome calling using ATAC-seq
Language:Python106 19 9231
GreenleafLab/10x-scATAC-2019
Publication Page for Satpathy*, Granja* et al 2019
Language:R92 9 1654
GreenleafLab/MPAL-Single-Cell-2019
Publication Page for MPAL Paper 2019
Language:R77 13 2538
GreenleafLab/motifmatchr
Fast motif matching in R
Language:C++43 11 911
GreenleafLab/brainchromatin
Code used to analyze single cell RNA and ATAC sequencing in developing human brain
Language:R31 4 167
GreenleafLab/NucleoATACR
R package for reading in & working with NucleoATAC outputs
Language:R26 10 212
GreenleafLab/scScalpChromatin
Language:R23 11 312
GreenleafLab/ArchR_2020
Publication Page for ArchR Manuscript 2020
Language:HTML22 9 139
GreenleafLab/ChrAccR
Analyzing chromatin accessibility data in R
Language:R18 9 197
GreenleafLab/Brain_ASD
Language:Python9 10 41
GreenleafLab/shareseq-pipeline
Language:Python5 9 22
GreenleafLab/LKB1_2021
Language:R3 9 02
GreenleafLab/NEAT-seq_reproducibility
Language:R3 10 12
GreenleafLab/SpearATAC_MS_2021
Language:R3 9 14
GreenleafLab/amplicon-smf
Code for processing single-molecule footprinting data on synthetic amplicons (from Doughty*, Hinks*, Schaepe*, et al. 2024).
Language:Python2 13 0
GreenleafLab/ImagingStationController
Hardware-control software for a sequencing flowcell imaging station based on GAIIx components
Language:Matlab2 9 01
GreenleafLab/puflibs
Language:Python2 9 00
GreenleafLab/snakeATAC_singularity
Language:Python2 13 0
GreenleafLab/array_analysis
Snakemake pipeline for Greenleaf lab array preprocessing.
Language:Python1 13 0
GreenleafLab/array_fitting_tools
Language:Python1 27 04
GreenleafLab/ChrAccRex
Example data for ChrAccR
Language:R1 3 0
GreenleafLab/matcha
Python library for fast barcode matching in sequencing data
Language:Python1 10 01
GreenleafLab/nnn_paper
Analysis for "High-Throughput DNA melt measurements enable improved models of DNA folding thermodynamics".
Language:Jupyter Notebook1 13 0
GreenleafLab/ArchR_Website
Language:CSS0 9 03
GreenleafLab/TtAgo
Language:Python0 10 00
GreenleafLab/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
Language:Python
GreenleafLab/lab-wiki
Repository to hold the lab wiki
10 0
GreenleafLab/synthetic_enhancer_footprinting_additional_materials
Additional files for the analysis of Doughty*, Hinks*, Schaepe*, et al. Nature 2024.
Language:Jupyter Notebook