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2020-sn-muscle

2021-03-sn-muscle

2021_islet-rfx6

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

atacseq-snakemake

Standard Parker Lab ATAC-seq processing pipeline in Snakemake form

atactk

A toolkit for working with ATAC-seq data.

ataqv

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

ataqv-2019

bioinf525

ATAC-seq lab for BIOINF525

bioinf545

ATAC-seq lab for BIOINF545

bmo

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

chromatin_information

A companion repository to our chromatin information manuscript

cta

C++ implementation of Buenrostro adapter trimming

danforth-2018

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

dna_protein_contacts

drmr

A tool for submitting pipeline scripts to distributed resource managers.

encodegsc

Genome Structure Correction

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

islet_sci-atac-seq_2019

Code accompanying Islet sci-ATAC-seq project

magic_final

MAGIC glycemic GWAS enrichment in annotations

mka

A tool for generating analysis pipelines from templates.

pillownet

U-Net for genomics

regulatoryannotations_comparisons

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

sn_muscle_2023

Code for snATAC + snRNA analyses

starr-seq-analysis-pipeline

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

yamda

Yet Another Motif Discovery Algorithm