The Parker Lab at the University of Michigan

All

29 repositories

ataqv
Public
A toolkit for QC and visualization of ATAC-seq results.
visualization quality-control tool software atac-seq
C++
•
GNU General Public License v3.0
•10•66•4•0•Updated Oct 14, 2024Oct 14, 2024
cta
Public
C++ implementation of Buenrostro adapter trimming
tool software adapter-trimming
C++
•5•2•2•1•Updated Oct 14, 2024Oct 14, 2024
Multiome-Doublet-Detection-NextFlow
Public
Python
•2•0•0•0•Updated Aug 29, 2024Aug 29, 2024
snRNAseq-NextFlow
Public
Nextflow
•3•0•0•0•Updated Jul 24, 2024Jul 24, 2024
atactk
Public
A toolkit for working with ATAC-seq data.
toolkit atac-seq footprinting adapter-trimming centipede
Python
•
GNU General Public License v3.0
•4•24•2•0•Updated Jun 11, 2024Jun 11, 2024
bioinf545
Public
ATAC-seq lab for BIOINF545
class atac-seq
Shell
•13•25•0•0•Updated Mar 12, 2024Mar 12, 2024
sn_muscle_2023
Public
Code for snATAC + snRNA analyses
Python
•0•0•0•0•Updated Nov 8, 2023Nov 8, 2023
BMO
Public
BMO - a tool for predicting TF binding from ATAC-seq data
R
•
GNU General Public License v3.0
•1•9•1•0•Updated Jun 7, 2022Jun 7, 2022
chromatin_information
Public
A companion repository to our chromatin information manuscript
Python
•1•2•0•0•Updated Mar 2, 2022Mar 2, 2022
2021_islet-rfx6
Public
Code for Walker, Saunders, Rai et al., (2021).
gwas rna-seq atac-seq single-cell integrative-analysis codex alpha-cell pancreas wgcna beta-cells
Roff
•0•2•0•0•Updated Feb 2, 2022Feb 2, 2022
2021-03-sn-muscle
Public
HTML
•1•0•0•0•Updated Sep 13, 2021Sep 13, 2021
magic_final
Public
MAGIC glycemic GWAS enrichment in annotations
Rebol
•1•1•0•0•Updated Mar 15, 2021Mar 15, 2021
ATACseq-Snakemake
Public
Standard Parker Lab ATAC-seq processing pipeline in Snakemake form
Python
•4•6•0•0•Updated Feb 9, 2021Feb 9, 2021
2020-sn-muscle
Public
Shell
•3•1•0•0•Updated Jul 1, 2020Jul 1, 2020
islet_sci-ATAC-seq_2019
Public
Code accompanying Islet sci-ATAC-seq project
bioinformatics snakemake single-cell
Python
•3•6•0•0•Updated Jan 20, 2020Jan 20, 2020
islet_cage
Public
Analyses of human pancreatic islet CAGE data
Python
•2•0•0•0•Updated Nov 21, 2019Nov 21, 2019
ataqv-2019
Public
Python
•0•1•0•0•Updated Nov 16, 2019Nov 16, 2019
PillowNet
Public
U-Net for genomics
Python
•
MIT License
•1•2•0•0•Updated Sep 29, 2019Sep 29, 2019
GenomeLoader
Public
A lightweight tool for loading genomic data in deep learning applications
Python
•
MIT License
•2•0•0•0•Updated Apr 17, 2019Apr 17, 2019
STARR-seq-Analysis-Pipeline
Public
Commands Template and Module for Automated Analysis of STARR-seq data.
template pipeline tool software starr-seq
Python
•1•4•0•0•Updated Feb 15, 2019Feb 15, 2019
dna_protein_contacts
Public
Python
•1•0•0•0•Updated Feb 1, 2019Feb 1, 2019
YAMDA
Public
Yet Another Motif Discovery Algorithm
bioinformatics biology motif-discovery motif-prediction
Python
•
MIT License
•7•2•0•0•Updated Jan 23, 2019Jan 23, 2019
regulatoryAnnotations_comparisons
Public
Comparison of Super/Stretch enhancers, HOT regions and Broad Domains.
Jupyter Notebook
•1•1•0•0•Updated Sep 11, 2018Sep 11, 2018
danforth-2018
Public
Recreate the computational analyses from Orchard, White, Thomas et al
Python
•1•1•0•0•Updated Jan 23, 2018Jan 23, 2018
homebrew-tap
Public
Homebrew tap for software from the Parker Lab at the University of Michigan
homebrew software
Ruby
•0•0•1•0•Updated Dec 8, 2017Dec 8, 2017
mka
Public
A tool for generating analysis pipelines from templates.
pipeline tool software
Python
•
GNU General Public License v3.0
•1•1•0•0•Updated Aug 17, 2017Aug 17, 2017
drmr
Public
A tool for submitting pipeline scripts to distributed resource managers.
pipeline tool slurm software pbs workload-automation
Python
•
GNU General Public License v3.0
•2•3•0•0•Updated May 9, 2017May 9, 2017
encodegsc
Public
Genome Structure Correction
software
Python
•2•2•0•0•Updated Jan 19, 2017Jan 19, 2017
bioinf525
Public
ATAC-seq lab for BIOINF525
class atac-seq
Shell
•10•10•0•0•Updated Mar 31, 2016Mar 31, 2016