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
29repos
3stars
6followers
Lilly conda-forge Noobies Tennis
organizations

Repositories I’ve built or contributed to significantly.

EliLillyCo/surmount5-proteomics
Analysis code for the SURMOUNT-5 proteomics study. Author.
Python R
T1D_snATAC
snATAC-seq of pancreas and type 1 diabetes risk loci.
2
Gaulton-Lab/pipelines
ATAC-seq, GWAS, and epigenomic analysis pipelines.
Python Jupyter Notebook
joshchiou.github.io
Source for this website, with automated data pipelines.
HTML SCSS JavaScript 1
conda-forge/r-mmrm-feedstock
conda-forge feedstock for r-mmrm. Maintainer.
Shell Batchfile 1 1

Open-source contributions

Selected merged pull requests to community scientific software.

Type:
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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 crashed the Home Assistant integration when the SunPower PVS serial number was 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, so it can be installed as a conda dependency in clinical trial 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 step that normalizes variant IDs before rsID assignment, which prevents mapping errors in GWAS summary statistics.
    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 the group export function so it works with updated dependencies.
    View pull request

  • 2022

  • Add filter for duplicate credible sets  ·  FinucaneLab/fine-mapping-inf  ·  2022-11-09
    feature Python
    Added a step that removes duplicate credible sets from fine-mapping output.
    View pull request
See all merged pull requests →