Files in mcalgaro93/benchdamic
Benchmark of differential abundance methods on microbiome data
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/DA_ALDEx2.R
R/DA_ANCOM.R
R/DA_DESeq2.R
R/DA_MAST.R
R/DA_Maaslin2.R
R/DA_NOISeq.R
R/DA_Seurat.R
R/DA_ZicoSeq.R
R/DA_basic.R
R/DA_corncob.R
R/DA_dearseq.R
R/DA_edgeR.R
R/DA_limma.R
R/DA_linda.R
R/DA_metagenomeSeq.R
R/DA_mixMC.R
R/GOF.R
R/TIEC.R
R/concordance.R
R/enrichment.R
R/fitDistribution.R
R/microbial_metabolism.R
R/norm_CSS.R
R/norm_DESeq2.R
R/norm_TSS.R
R/norm_edgeR.R
R/plotConcordance.R
R/plotEnrichment.R
R/plotGOF.R
R/plotTIEC.R
R/ps_plaque_16S.R
R/ps_stool_16S.R
R/runDA.R
R/runNormalizations.R
R/utilities.R
R/weights_ZINB.R
README.md
data/microbial_metabolism.RData
data/ps_plaque_16S.RData
data/ps_stool_16S.RData
inst/CITATION
man/CAT.Rd
man/DA_ALDEx2.Rd
man/DA_ANCOM.Rd
man/DA_DESeq2.Rd
man/DA_MAST.Rd
man/DA_Maaslin2.Rd
man/DA_NOISeq.Rd
man/DA_Seurat.Rd
man/DA_ZicoSeq.Rd
man/DA_basic.Rd
man/DA_corncob.Rd
man/DA_dearseq.Rd
man/DA_edgeR.Rd
man/DA_limma.Rd
man/DA_linda.Rd
man/DA_metagenomeSeq.Rd
man/DA_mixMC.Rd
man/RMSE.Rd
man/addKnowledge.Rd
man/areaCAT.Rd
man/checkNormalization.Rd
man/createColors.Rd
man/createConcordance.Rd
man/createEnrichment.Rd
man/createMocks.Rd
man/createPositives.Rd
man/createSplits.Rd
man/createTIEC.Rd
man/enrichmentTest.Rd
man/extractDA.Rd
man/extractStatistics.Rd
man/fitDM.Rd
man/fitHURDLE.Rd
man/fitModels.Rd
man/fitNB.Rd
man/fitZIG.Rd
man/fitZINB.Rd
man/getDA.Rd
man/getPositives.Rd
man/getStatistics.Rd
man/get_counts_metadata.Rd
man/iterative_ordering.Rd
man/meanDifferences.Rd
man/microbial_metabolism.Rd
man/norm_CSS.Rd
man/norm_DESeq2.Rd
man/norm_TSS.Rd
man/norm_edgeR.Rd
man/plotConcordance.Rd
man/plotConcordanceDendrogram.Rd
man/plotConcordanceHeatmap.Rd
man/plotContingency.Rd
man/plotEnrichment.Rd
man/plotFDR.Rd
man/plotFPR.Rd
man/plotKS.Rd
man/plotLogP.Rd
man/plotMD.Rd
man/plotMutualFindings.Rd
man/plotPositives.Rd
man/plotQQ.Rd
man/plotRMSE.Rd
man/prepareObserved.Rd
man/ps_plaque_16S.Rd
man/ps_stool_16S.Rd
man/runDA.Rd
man/runMocks.Rd
man/runNormalizations.Rd
man/runSplits.Rd
man/setNormalizations.Rd
man/set_ALDEx2.Rd
man/set_ANCOM.Rd
man/set_DESeq2.Rd
man/set_MAST.Rd
man/set_Maaslin2.Rd
man/set_NOISeq.Rd
man/set_Seurat.Rd
man/set_ZicoSeq.Rd
man/set_basic.Rd
man/set_corncob.Rd
man/set_dearseq.Rd
man/set_edgeR.Rd
man/set_limma.Rd
man/set_linda.Rd
man/set_metagenomeSeq.Rd
man/set_mixMC.Rd
man/weights_ZINB.Rd
tests/testthat.R
tests/testthat/test_ANCOM.R
tests/testthat/test_DA.R
tests/testthat/test_DA_ALDEx2.R
tests/testthat/test_DA_paired.R
tests/testthat/test_createMocks.R
tests/testthat/test_createSplits.R
tests/testthat/test_getStatistics_getDA_extractDA.R
tests/testthat/test_get_counts_metadata.R
tests/testthat/test_normalizations.R
tests/testthat/test_set_ALDEx2.R
vignettes/GOF_structure.svg
vignettes/TIEC_structure.svg
vignettes/benchdamic_methods.csv
vignettes/bib_intro.json
vignettes/bioinformatics.csl
vignettes/concordance_structure.svg
vignettes/enrichment_structure.svg
vignettes/intro.Rmd
vignettes/norm_DA_structure.svg
