code

A slice of my public coding activity. Most production work lives in enterprise GitHub organizations (Pfizer, Lilly) and is not reflected here.

GitHub avatar
Josh Chiou
27repos
2stars
5followers
Eli Lilly conda-forge Noobies Tennis
organizations

Repositories I’ve built or contributed to significantly.

T1D_snATAC
Data and analysis code for snATAC-seq profiling of pancreatic islets and T1D risk loci.
2
Gaulton-Lab/pipelines
Pipelines for bulk and single-cell ATAC-seq, GWAS, and epigenomic analysis.
joshchiou.github.io
Personal academic website — Jekyll/al-folio with automated data pipelines.
HTML 1
conda-forge/r-mmrm-feedstock
conda-forge feedstock for r-mmrm (Mixed Models for Repeated Measures). Maintainer.
Shell 1 1

Open-source contributions

Selected merged pull requests to community scientific software.

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  • 2026

  • fix: prevent memory leak crash when PVS serial is an IP address  ·  smcneece/ha-esunpower  ·  2026-03-26
    bug fix Python
    Fixed a memory leak that caused the Home Assistant integration to crash when the SunPower PVS serial number is configured as an IP address.
    View pull request
  • Add r-mmrm: Mixed Models for Repeated Measures  ·  conda-forge/staged-recipes  ·  2026-02-12
    packaging R
    Packaged r-mmrm for conda-forge, making it available as a conda dependency for clinical trial analysis pipelines.
    View pull request

  • 2025

  • Parallel IDF  ·  scverse/SnapATAC2  ·  2025-07-09
    performance Python
    Parallelized inverse-document-frequency computation in dimensionality reduction, cutting runtime on large datasets.
    View pull request
  • Compatibility with rpy2  ·  stephenslab/susieR  ·  2025-02-27
    compatibility R
    Restored Python interoperability so susieR can be called from rpy2 pipelines.
    View pull request

  • 2024

  • add fix ID before assign rsID  ·  Cloufield/gwaslab  ·  2024-11-28
    bug fix Python
    Added a variant ID normalization step before rsID assignment, preventing downstream mapping errors in GWAS summary statistics workflows.
    View pull request
  • Fix for multiple harmony covariates  ·  scverse/SnapATAC2  ·  2024-10-06
    bug fix Python
    Fixed batch correction when more than one covariate is passed to Harmony integration.
    View pull request

  • 2023

  • Update GroupExport.R  ·  GreenleafLab/ArchR  ·  2023-08-25
    bug fix R
    Fixed group export function compatibility with updated dependencies.
    View pull request

  • 2022

  • Add filter for duplicate credible sets  ·  FinucaneLab/fine-mapping-inf  ·  2022-11-09
    feature Python
    Added deduplication step for credible sets output, preventing redundant entries in fine-mapping results.
    View pull request
See all merged pull requests →