Software

Open-source software I maintain or have contributed to

Most of my work is in R and Bioconductor, as part of the Orchestrating Microbiome Analysis project. Below are the main projects. For the rest of my work, see my GitHub profile.

Maintainer

Downloads per month, Oct 2025 to Sep 2026. For Bioconductor packages this is the number of distinct IP addresses (source); for CRAN packages, all downloads from the Posit CRAN mirror (source). The large number is the median month. Hover a bar for the exact number.

HoloFoodR Bioconductor
R interface to EBI HoloFood resource

GitHubRelease Devel

212 downloads/month

MGnifyR Bioconductor
R interface to EBI MGnify metagenomics resource

GitHubRelease Devel

242 downloads/month

mia Bioconductor
Microbiome analysis

GitHubRelease Devel

2,755 downloads/month

miaTime Bioconductor
Microbiome time series analysis

GitHubRelease Devel

210 downloads/month

miaViz Bioconductor
Microbiome analysis plotting and visualization

GitHubRelease Devel

629 downloads/month

OMA Bioconductor
Orchestrating Microbiome Analysis with Bioconductor, an open online book

Contributor

anansi Bioconductor
Annotation-based analysis of specific interactions

GitHubRelease Devel

176 downloads/month

bluster Bioconductor
Clustering algorithms for Bioconductor

GitHubRelease Devel

9,536 downloads/month

IntegratedLearner GitHub
Integrated multi-omics learning for survival and other outcomes

miaSim Bioconductor
Microbiome data simulation

GitHubRelease Devel

302 downloads/month

mikropml CRAN
User-friendly R package for supervised machine learning pipelines

500 downloads/month

MsExperiment Bioconductor
Infrastructure for mass spectrometry experiments

GitHubRelease Devel

1,688 downloads/month

scater Bioconductor
Single-cell analysis toolkit for gene expression data in R

GitHubRelease Devel

11,254 downloads/month

TreeSummarizedExperiment Bioconductor
S4 class for data with tree structures

GitHubRelease Devel

3,115 downloads/month

vegan CRAN
Community ecology package

143,326 downloads/month