The Parker Lab at the University of Michigan

ataqv

A toolkit for QC and visualization of ATAC-seq results.

atactk

A toolkit for working with ATAC-seq data.

bioinf545

ATAC-seq lab for BIOINF545

bioinf525

ATAC-seq lab for BIOINF525

BMO

BMO - a tool for predicting TF binding from ATAC-seq data

ATACseq-Snakemake

Standard Parker Lab ATAC-seq processing pipeline in Snakemake form

islet_sci-ATAC-seq_2019

Code accompanying Islet sci-ATAC-seq project

STARR-seq-Analysis-Pipeline

Commands Template and Module for Automated Analysis of STARR-seq data.

drmr

A tool for submitting pipeline scripts to distributed resource managers.

2021_islet-rfx6

Code for Walker, Saunders, Rai et al., (2021).

chromatin_information

A companion repository to our chromatin information manuscript

cta

C++ implementation of Buenrostro adapter trimming

encodegsc

Genome Structure Correction

PillowNet

U-Net for genomics

YAMDA

Yet Another Motif Discovery Algorithm

2020-sn-muscle

ataqv-2019

danforth-2018

Recreate the computational analyses from Orchard, White, Thomas et al

magic_final

MAGIC glycemic GWAS enrichment in annotations

mka

A tool for generating analysis pipelines from templates.

regulatoryAnnotations_comparisons

Comparison of Super/Stretch enhancers, HOT regions and Broad Domains.

2021-03-sn-muscle

dna_protein_contacts

GenomeLoader

A lightweight tool for loading genomic data in deep learning applications

homebrew-tap

Homebrew tap for software from the Parker Lab at the University of Michigan

islet_cage

Analyses of human pancreatic islet CAGE data

sn_muscle_2023

Code for snATAC + snRNA analyses