Benchmark of differential abundance methods on microbiome data
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Documentation for package ‘benchdamic’ version 1.11.0
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_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_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 |