# Benchmark of differential abundance methods on microbiome data

## Documentation for package ‘benchdamic’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

addKnowledge | addKnowledge
areaCAT | areaCAT
CAT | CAT
checkNormalization | checkNormalization
createColors | createColors
createConcordance | createConcordance
createEnrichment | createEnrichment
createMocks | createMocks
createPositives | createPositives
createSplits | createSplits
createTIEC | createTIEC
DA_ALDEx2 | DA_ALDEx2
DA_ANCOM | DA_ANCOM
DA_basic | DA_basic
DA_corncob | DA_corncob
DA_dearseq | DA_dearseq
DA_DESeq2 | DA_DESeq2
DA_edgeR | DA_edgeR
DA_limma | DA_limma
DA_linda | DA_linda
DA_Maaslin2 | DA_Maaslin2
DA_maaslin3 | DA_maaslin3
DA_MAST | DA_MAST
DA_metagenomeSeq | DA_metagenomeSeq
DA_mixMC | DA_mixMC
DA_NOISeq | DA_NOISeq
DA_Seurat | DA_Seurat
DA_ZicoSeq | DA_ZicoSeq
enrichmentTest | enrichmentTest
extractDA | extractDA
extractStatistics | extractStatistics
fitDM | fitDM
fitHURDLE | fitHURDLE
fitModels | fitModels
fitNB | fitNB
fitZIG | fitZIG
fitZINB | fitZINB
getDA | getDA
getPositives | getPositives
getStatistics | getStatistics
get_counts_metadata | get_counts_metadata
iterative_ordering | iterativeOrdering
meanDifferences | meanDifferences
microbial_metabolism | (Data) Microbial metabolism
norm_CSS | norm_CSS
norm_DESeq2 | norm_DESeq2
norm_edgeR | norm_edgeR
norm_TSS | norm_TSS
plotConcordance | plotConcordance
plotContingency | plotContingency
plotEnrichment | plotEnrichment
plotFDR | plotFDR
plotFPR | plotFPR
plotKS | plotKS
plotLogP | plotLogP
plotMD | plotMD
plotMutualFindings | plotMutualFindings
plotPositives | plotPositives
plotQQ | plotQQ
plotRMSE | plotRMSE
prepareObserved | prepareObserved
ps_plaque_16S | (Data) 60 Gingival Plaque samples of 16S rRNA (HMP 2012)
ps_stool_16S | (Data) 33 Stool samples of 16S rRNA (HMP 2012)
RMSE | RMSE
runDA | runDA
runMocks | runMocks
runNormalizations | runNormalizations
runSplits | runSplits
setNormalizations | setNormalizations
set_ALDEx2 | set_ALDEx2
set_ANCOM | set_ANCOM
set_basic | set_basic
set_corncob | set_corncob
set_dearseq | set_dearseq
set_DESeq2 | set_DESeq2
set_edgeR | set_edgeR
set_limma | set_limma
set_linda | set_linda
set_Maaslin2 | set_Maaslin2
set_maaslin3 | set_maaslin3
set_MAST | set_MAST
set_metagenomeSeq | set_metagenomeSeq
set_mixMC | set_mixMC
set_NOISeq | set_NOISeq
set_Seurat | set_Seurat
set_ZicoSeq | set_ZicoSeq
weights_ZINB | weights_ZINB