Software

I am the main developer for these packages:

SIAMCAT
R package for Statistical Inference of Associations between Microbial Communities And host phenoType
Github repository

BAMBI/SIMBA
R packages for the simulation of microbiome and the evaluation of differential abundance testing methods
BAMBI Github repository and SIMBA Github repository

Additionally, I contributed to these packages:

PhaVa
python package for identifying phase variable invertible regions in bacterial genomes using long-read sequencing
Github repository
Developed by Patrick T West, see this preprint

PHONEMeS
R package to model signalling networks based on untargeted phosphoproteomic data
Github repository
Originally developed by Camille DA Terfve, see this publication

kinact
python Toolbox for Kinase Activity Scoring based on phosphoproteomic data
Github repository
Now part of OmniPath package developed by Dénes Türei, see the OmniPath Github repo