Benchmark of differential abundance methods on microbiome data


[Up] [Top]

Documentation for package ‘benchdamic’ version 1.0.0

Help Pages

addKnowledge addKnowledge
areaCAT areaCAT
checkNormalization checkNormalization
createColors createColors
createConcordance createConcordance
createEnrichment createEnrichment
createMocks createMocks
createPositives createPositives
createSplits createSplits
createTIEC createTIEC
DA_ALDEx2 DA_ALDEx2
DA_corncob DA_corncob
DA_DESeq2 DA_DESeq2
DA_edgeR DA_edgeR
DA_limma DA_limma
DA_MAST DA_MAST
DA_metagenomeSeq DA_metagenomeSeq
DA_Seurat DA_Seurat
enrichmentTest enrichmentTest
extractDA extractDA
extractStatistics extractStatistics
fitDM fitDM
fitHURDLE fitHURDLE
fitModels fitModels
fitNB fitNB
fitZIG fitZIG
fitZINB fitZINB
getDA getDA
getPositives getPositives
getStatistics getStatistics
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
plotFPR plotFPR
plotKS plotKS
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_corncob set_corncob
set_DESeq2 set_DESeq2
set_edgeR set_edgeR
set_limma set_limma
set_MAST set_MAST
set_metagenomeSeq set_metagenomeSeq
set_Seurat set_Seurat
weights_ZINB weights_ZINB