A package for running lefse and microbiomeMarker on MicrobiomeBenchmarkData

Install this package in R

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("waldronlab/MicrobiomeBenchmarkDataLefse")

Lefse (conda version)

Check the inst/scripts for source code. Check the inst/extdata directory for results.

Install lefse from bioconda

conda create -n lefse
conda activate lefse
## conda config --set channel_priority flexible # This might be necessary
conda install -c bioconda lefse

Workflow

1. Generate the gingival.txt file:

## R dependencies must be installed
Rscript --vanilla getData.R

2. Run the script:

## conda activate lefse 
./runLefse.sh

3. Deactivate session when the job is done:

conda deactivate

.res file names

• a = anova threshold
• w = wilcoxon threshold
• lda = lda threshold
• it = iteration
• bp = bootstrap