Files in mcalgaro93/benchdamic

Benchmark of differential abundance methods on microbiome data

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 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/intro.Rmd