Skip to content

@ParkerLab The Parker Lab at the University of Michigan

Change the repository type filter

All

    Repositories list

    37 repositories

    • muscle_nfr_nucQTL

      Public
      Python
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • sn_muscle_2023

      Public
      Code for snATAC + snRNA analyses
      Python
      •0•1•0•0•Updated Apr 9, 2026Apr 9, 2026

    • TSS_MPRA_2026

      Public
      Code used to run elastic net, generalized linear models, and MPRAnalyze sub-analyses and interaction model for Bose et. al. 2026 islet TSS MPRA paper. DOI: 10.1…
      R
      •
      MIT License
      •1•0•0•0•Updated Apr 9, 2026Apr 9, 2026

    • FAP_paper

      Public
      Discovering stimulatory state specific type 2 diabetes GWAS mechanisms with single-cell multi-omics on iPSC-derived fibro-adipogenic progenitors
      Jupyter Notebook
      •0•0•0•0•Updated Mar 31, 2026Mar 31, 2026

    • bioinf545

      Public
      ATAC-seq lab for BIOINF545
      classatac-seq
      classatac-seq
      Shell
      •13•24•0•0•Updated Feb 17, 2026Feb 17, 2026

    • atactk

      Public
      A toolkit for working with ATAC-seq data.
      toolkitatac-seqfootprinting
      toolkitatac-seqfootprintingadapter-trimmingcentipede
      Python
      •
      GNU General Public License v3.0
      •4•24•2•1•Updated Jan 22, 2026Jan 22, 2026

    • PanKbase-DEG-analysis

      Public
      Collection of code and documentation to replicate islet DEG analysis on PanKbase.
      Jupyter Notebook
      •2•0•0•0•Updated Aug 28, 2025Aug 28, 2025

    • PanKbase-scRNA-seq

      Public
      Collection of code and documentation to replicate islet single cell map on PanKbase.
      Jupyter Notebook
      •2•1•0•0•Updated Jun 11, 2025Jun 11, 2025

    • PanKgraph-finemap-coloc

      Public
      Collection of code and documentation to conduct fine-mapping and colocalization analysis for PanKbase and PanKgraph.
      Jupyter Notebook
      •2•0•0•0•Updated Jun 6, 2025Jun 6, 2025

    • albanus_2020_nih_islets_sn_t1d

      Public
      snATAC-seq + scRNA-seq analyses of healthy and AAB+ human islets
      Jupyter Notebook
      •0•0•0•0•Updated Jun 1, 2025Jun 1, 2025

    • Multiome-Doublet-Detection-NextFlow

      Public
      Python
      •4•0•0•0•Updated Apr 4, 2025Apr 4, 2025

    • snakemake-multiome-preprocessing

      Public
      Automates setup of configs and execution of preprocessing steps for a multiome library.
      Python
      •1•0•0•0•Updated Mar 31, 2025Mar 31, 2025

    • snRNAseq-NextFlow

      Public
      Nextflow
      •5•1•0•0•Updated Feb 10, 2025Feb 10, 2025

    • ataqv

      Public
      A toolkit for QC and visualization of ATAC-seq results.
      visualizationquality-controltool
      visualizationquality-controltoolsoftwareatac-seq
      C++
      •
      GNU General Public License v3.0
      •11•74•4•0•Updated Jan 8, 2025Jan 8, 2025

    • cta

      Public
      C++ implementation of Buenrostro adapter trimming
      toolsoftwareadapter-trimming
      toolsoftwareadapter-trimming
      C++
      •5•2•2•1•Updated Oct 14, 2024Oct 14, 2024

    • 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).
      gwasrna-seqatac-seq
      gwasrna-seqatac-seqsingle-cellintegrative-analysiscodexalpha-cellpancreaswgcnabeta-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
      •0•1•0•0•Updated Mar 15, 2021Mar 15, 2021

    • ATACseq-Snakemake

      Public
      Standard Parker Lab ATAC-seq processing pipeline in Snakemake form
      Python
      •4•7•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
      bioinformaticssnakemakesingle-cell
      bioinformaticssnakemakesingle-cell
      Python
      •3•5•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.
      templatepipelinetool
      templatepipelinetoolsoftwarestarr-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
      bioinformaticsbiologymotif-discovery
      bioinformaticsbiologymotif-discoverymotif-prediction
      Python
      •
      MIT License
      •7•2•0•0•Updated Jan 23, 2019Jan 23, 2019
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.