GreenleafLab

All

33 repositories

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
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MIT License
•64•0•0•0•Updated Nov 30, 2024Nov 30, 2024
ArchR
Public
ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
R
•
MIT License
•140•390•135•17•Updated Nov 28, 2024Nov 28, 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 Nov 18, 2024Nov 18, 2024
array_analysis
Public
Snakemake pipeline for Greenleaf lab array preprocessing.
Python
•0•1•0•0•Updated Nov 18, 2024Nov 18, 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
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MIT License
•0•2•0•0•Updated Sep 25, 2024Sep 25, 2024
chromVAR
Public
chromatin Variability Across Regions (of the genome!)
bioinformatics dnase-seq r atac-seq
R
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Other
•38•162•77•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
bioinformatics r motif-discovery
C++
•
GNU General Public License v3.0
•11•43•7•1•Updated Jan 24, 2024Jan 24, 2024
scScalpChromatin
Public
R
•12•23•0•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•3•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
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MIT License
•2•3•0•0•Updated Jun 27, 2021Jun 27, 2021
SpearATAC_MS_2021
Public
R
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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
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GNU General Public License v3.0
•1•1•0•0•Updated Jan 3, 2021Jan 3, 2021
NucleoATAC
Public
nucleosome calling using ATAC-seq
bioinformatics nuclesosome atac-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
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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
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Apache License 2.0
•1•2•0•0•Updated Jul 5, 2018Jul 5, 2018