API for RIVM-IIV-Microbiome/biomeUtils
Utilities for microbiome analytics
| Global functions | |
|---|---|
| .check_col_sam_data | Source code |
| .check_decimal | Source code |
| .check_names_dup | Source code |
| .check_rank_single | Source code |
| .check_ranks | Source code |
| .check_refseq | Source code |
| .check_taxa | Source code |
| .count_tax_tib | Source code |
| .select_cols_abundance | Source code |
| .select_cols_sample | Source code |
| .select_cols_taxonomy | Source code |
| .select_rows_abundance | Source code |
| .select_rows_sample | Source code |
| .select_rows_taxonomy | Source code |
| .summarizeTaxonomicAssignmentsDF | Source code |
| FuentesIliGutData | Man page |
| SprockettTHData | Man page |
| biomeUtils-package | Man page |
| buildSeqTree | Man page Source code |
| calculatePD | Man page Source code |
| calculateQC | Man page Source code |
| calculateTaxaFoldDifference | Man page Source code |
| checkAbundanceCutOffs | Man page Source code |
| checkFilterEffect | Man page |
| checkPolyphyletic | Man page Source code |
| checkPrevalenceCutOffs | Man page Source code |
| cleanTaxonomy | Man page Source code |
| comparePhyloseq | Man page Source code |
| fetchSequence | Man page Source code |
| filterPhyloseq | Man page |
| filterSampleByNames | Man page Source code |
| filterSampleData | Man page Source code |
| filterTaxaByNames | Man page Source code |
| filterTaxaData | Man page Source code |
| filterTaxaTotal | Man page Source code |
| findTopTaxa | Man page Source code |
| genericUtilities | Man page |
| getAbundanceTibble | Man page Source code |
| getCLR | Man page Source code |
| getOtuTableFromTibble | Man page Source code |
| getPhyloseqSlots | Man page |
| getPrevalence | Man page Source code |
| getProportions | Man page Source code |
| getSampleTableFromTibble | Man page Source code |
| getSampleTibble | Man page Source code |
| getTaxaOverview | Man page Source code |
| getTaxaSummary | Man page Source code |
| getTaxaTableFromTibble | Man page Source code |
| getTaxaTibble | Man page Source code |
| getTibble | Man page |
| getYCTheta | Man page Source code |
| meltAbundance | Man page Source code |
| meltDistanceToTable | Man page Source code |
| mutateAbundanceTable | Man page Source code |
| mutatePhyloseq | Man page |
| mutateSampleData | Man page Source code |
| mutateTaxaTable | Man page Source code |
| pullPhyloseq | Man page |
| pullSampleAbundance | Man page Source code |
| pullTaxaAbundance | Man page Source code |
| pullTaxaRank | Man page |
| readMergedMetaphlan | Man page Source code |
| removeZeros | Man page Source code |
| renameSampleVariables | Man page Source code |
| saveAbundanceData | Man page Source code |
| saveData | Man page |
| saveSampleData | Man page Source code |
| saveSequence | Man page Source code |
| saveTaxonomyData | Man page Source code |
| separateSampleColumn | Man page Source code |
| summarizeTaxonomicAssignments | Man page Source code |
| transformation | Man page |
| transposeAbundance | Man page Source code |
| trendAbundanceAssignment | Man page Source code |
| uniqueness | Man page Source code |
| uniteGenusSpeciesNames | Man page Source code |
| uniteSampleColumn | Man page Source code |
