Man pages for waldronlab/BugSigDBStats
BugSigDB Stats and Analysis
| calcJaccardSimilarity | Calculate pairwise Jaccard similarity between all signatures |
| calcPairwiseOverlaps | Calculate pairwise overlaps between all signatures |
| calcSemanticSimilarity | Calculate semantic similarity |
| getMostFrequentTaxa | Get most frequent taxa |
| getNcbiTaxonomyObo | Get NCBI Taxonomy in OBO format |
| getTaxLevelDistribution | Get distribution of taxonomic levels |
| getTaxonStats | Taxon stats |
| makeDist | Title Create a Jaccard or overlap dissimilarity matrix from... |
| microbeHeatmap | Plot microbe co-occurrence in a heatmap |
| paperStat | Paper stats |
| plotComposition | Plot composition of a table of a categorical variable |
| plotCuratorStats | Plot curation output for each curator |
| plotProgressOverTime | Plot curation output as a function of time |
| plotUniqueMicrobesOverTime | Plot curation output for each curator |
| pmid2pubyear | Get the publication year for a PMID |
| sigStat | Signature stats |
| stratifyByCurator | Stratify curation output by curator |
| stripEmptySignatures | Remove entries that do not contain signatures |
| syncWithNCBI | Synchronize signatures with NCBI Taxonomy |
| tabCol | Table column |
| tabDiv | Table diversity column |
| testAssociation | Test association of a taxon with a certain category of a... |
| testReplicability | Test replicability of microbiome changes across studies |
| weightedBMA | Weighted semantic similarity |
