Repositories list

• bioinf545

  Public
  ATAC-seq lab for BIOINF545

  classatac-seq

  classatac-seq

  Shell

  •13•24•0•0•Updated Feb 17, 2026Feb 17, 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 Jan 29, 2026Jan 29, 2026

• atactk

  Public
  A toolkit for working with ATAC-seq data.

  toolkitatac-seqfootprinting+ 2

  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

• muscle_nfr_nucQTL

  Public
  Python

  •0•0•0•0•Updated Jun 9, 2025Jun 9, 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+ 2

  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

• sn_muscle_2023

  Public
  Code for snATAC + snRNA analyses

  Python

  •0•1•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).

  gwasrna-seqatac-seq+ 10

  gwasrna-seqatac-seqsingle-cellintegrative-analysiscodexalpha-cellpancreaswgcnabeta-cells+ 3

  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+ 2

  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+ 1

  bioinformaticsbiologymotif-discoverymotif-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