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1. lorepy lorepy Public

   A library to create lore plots (logistic regression of the prevalence of a categorical variable in function of a continuous feature)

   Python 12 2

2. covid19_respiratory_microbiome covid19_respiratory_microbiome Public

   Code accompanying the manuscript "Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host"

   R 3 3

3. benchmark_microbiome_transformations benchmark_microbiome_transformations Public

   Forked from vllorens/benchmark_microbiome_transformations

   Code to reproduce the analyses from the paper "Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases"

   R 8 1

4. omixer-rpm omixer-rpm Public

   A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.

   Java 24 8

5. GMMs GMMs Public

   A manually curated database of human gut metabolic modules.

   15 5

6. QMP QMP Public

   Quantitative Microbiome Profiling

   R 15 8