HoMiStats

Statistics tools for host-microbiome dual transcriptomics

Installation

devtools::install_github("sterrettJD/HoMiStats")

Package capabilities

Statistical modules

HoMiStats consists of two main modules:

1. Metatranscriptomics differential expression (mtxDE implemented in run_mtxDE())

   • Zero inflated beta regression, motivated by this review and using a model inspired by Peng et al., 2016
     • Implemented via GAMLSS BEZI and ZIBR (supports random effects)
   • Linear regression and linear mixed-effects regression

2. Construction of correlation network between host and microbial transcripts (HoMiCorr implemented in run_HoMiCorr())

   • Also supports both zero inflated beta regression (gamlss or ZIBR for random effects) and linear regression or linear mixed-effects regression

Utilities

HoMiStats contains tools for transforming metatranscriptomic data, as well as tools for filtering genes based on low expression, prevalence, or variance.