Repositories list

• PheMINE

  Public
  PheMINE is a reproducible, automated workflow for analyzing electronic health records. It streamlines cohort construction, performs permutation-based phecode en…

  machine-learningicd-10icd-9+ 4

  machine-learningicd-10icd-9ehr-phenotypingsnakemake-workflowshapley-valuephenome-wide

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• drive

  Public
  A cli tool to analyze ibd sharing for a specific locus for multiple phenotypes

  Python

  •

  Apache License 2.0

  •33 forks•00 stars•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• COMPADRE

  Public
  Pedigree generation software incorporating PRIMUS, ERSA, and PADRE.

  pythonbioinformaticsgenetics+ 10

  pythonbioinformaticsgeneticsperlpopulation-geneticsgenotype-datarelatednessidentity-by-descenthuman-geneticsheredity+ 3

  Perl

  •11 fork•33 stars•00 issues•11 pull request•Updated Apr 9, 2026Apr 9, 2026

• SURVIVOR

  Public
  Toolset for SV simulation, comparison and filtering

  C++

  •

  MIT License

  •5151 forks•00 stars•00 issues•00 pull requests•Updated Mar 18, 2026Mar 18, 2026

• CCHC_proteomics_QC

  Public
  QC of CCHC proteomics batch2

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 13, 2026Jan 13, 2026

• pedigree-simulator

  Public
  Pedigree simulation software tool

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 22, 2025Nov 22, 2025

• hap-ibd

  Public
  The hap-ibd program detects identity-by-descent segments in phased genotype data.

  Java

  •1010 forks•00 stars•00 issues•11 pull request•Updated Nov 21, 2025Nov 21, 2025

• Nextflow

  Public
  Nextflow workflows - initially established to run ExpansionHunter

  00 forks•00 stars•00 issues•00 pull requests•Updated Oct 8, 2025Oct 8, 2025

• ExpansionHunter

  Public
  A tool for estimating repeat sizes

  C++

  •

  Other

  •6565 forks•00 stars•00 issues•00 pull requests•Updated Oct 8, 2025Oct 8, 2025

• RNAseq_pipeline

  Public
  Below lab RNAseq QC pipeline

  C++

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 19, 2025Aug 19, 2025

• compadre-website

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 22, 2025Jul 22, 2025

• Tractor

  Public
  Scripts for implementing the Tractor pipeline

  Jupyter Notebook

  •

  MIT License

  •1515 forks•00 stars•00 issues•00 pull requests•Updated May 27, 2025May 27, 2025

• ancQTL

  Public
  R

  •

  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 16, 2025May 16, 2025

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.9k3.9k forks•00 stars•00 issues•00 pull requests•Updated May 5, 2025May 5, 2025

• MetaXcan

  Public
  MetaXcan software and manuscript

  Python

  •

  Other

  •104104 forks•00 stars•00 issues•11 pull request•Updated Apr 29, 2025Apr 29, 2025

• Concordance-Analysis

  Public
  This analysis was performed to determine if there was concordance between our ancestries-specific GWAS summary statistics. Please see Shaw et al. 2021

  Python

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 24, 2025Apr 24, 2025

• ldsc

  Public
  LD Score Regression (LDSC)

  HTML

  •

  GNU General Public License v3.0

  •368368 forks•1616 stars•00 issues•00 pull requests•Updated Dec 16, 2024Dec 16, 2024

• bioindex-client

  Public
  Gets gene associations from Bioindex

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 18, 2024Oct 18, 2024

• rShiny_Bias

  Public
  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Sep 19, 2024Sep 19, 2024

• McBias

  Public
  McBias is an r package designed to help estimate the effects of bias found in large datasets of convenience

  R

  •22 forks•00 stars•00 issues•00 pull requests•Updated Sep 11, 2024Sep 11, 2024

• CCHC_lipidomics

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•11 pull request•Updated Aug 13, 2024Aug 13, 2024

• PyVCF3

  Public
  A Variant Call Format reader for Python.

  Python

  •

  Other

  •224224 forks•00 stars•00 issues•00 pull requests•Updated Aug 12, 2024Aug 12, 2024

• staged-recipes

  Public
  A place to submit conda recipes before they become fully fledged conda-forge feedstocks

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •5.9k5.9k forks•00 stars•00 issues•00 pull requests•Updated Aug 9, 2024Aug 9, 2024

• conda-forge-pinning-feedstock

  Public
  A conda-smithy repository for conda-forge-pinning.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •585585 forks•00 stars•00 issues•00 pull requests•Updated Jul 25, 2024Jul 25, 2024

• docker-builds

  Public
  :package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

  Dockerfile

  •

  GNU General Public License v3.0

  •137137 forks•00 stars•00 issues•00 pull requests•Updated Jul 18, 2024Jul 18, 2024

• xcftools

  Public
  Set of tools for handling XCF files

  C++

  •33 forks•00 stars•00 issues•00 pull requests•Updated Jul 18, 2024Jul 18, 2024

• htslib

  Public
  C library for high-throughput sequencing data formats

  C

  •

  Other

  •461461 forks•00 stars•00 issues•00 pull requests•Updated Jul 9, 2024Jul 9, 2024

• CCHC_transcriptomics

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated May 2, 2024May 2, 2024

• vcflib

  Public
  C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

  C++

  •

  MIT License

  •223223 forks•00 stars•00 issues•00 pull requests•Updated Apr 29, 2024Apr 29, 2024

• eQTL_with_GTEx_pipeline

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 22, 2024Apr 22, 2024