Man pages for microbiome/microbiomeold
Tools for microbiome analysis
| Bagged.RDA | Description: BAGGED RDA Bootstrap solutions that follows the... |
| Bagged.RDA.Feature.Selection | Description: BAGGED RDA feature selection |
| bootstrap.microbecount | bootstrap.microbecount |
| bootstrap.microbes | bootstrap.microbes |
| calculate.hclust | calculate.hclust |
| check.anova | Calculate ANOVA test (BH correction) for multi-group... |
| check_wilcoxon | Calculate Wilcoxon test (unpaired; BH correction) for the... |
| cmat2table | Arrange correlation matrices from cross.correlate into a... |
| coefficient.of.bimodality | Coefficient of bimodality |
| convert4corrwscatter | Interactive scatter plot |
| Core2D | Core2D |
| core_heatmap | core_heatmap |
| core.sum | core.sum |
| core.which | core.which |
| correlation.heatmap | correlation.heatmap |
| createCore | createCore |
| cross.correlate | Cross-correlate columns of the input matrices |
| densityplot | DensityPlot |
| distance.matrix | Calculate distance matrix between the _columns_ of the input... |
| estimate_stability | estimate_stability |
| estimate_variability | Stability analysis. Calculates average Pearson ' correlation... |
| GetPhylogeny | GetPhylogeny |
| get.probeset | get probeset data matrix |
| GKtau | Measure association between nominal (no order for levels)... |
| htree.plot | htree.plot |
| impute | Impute missing values from a Gaussian. |
| intermediate_stability | intermediate_stability |
| level1TOlevel0 | L1-L0 mappings |
| level2TOlevel0 | L2-L0 mappings |
| level2TOlevel1 | level2-level1 mappings |
| levelmap | levelmap |
| list.color.scales | List color scales |
| list_prevalent_groups | List prevalent groups |
| lower.triangle | Get lower triangle of a square matrix as a numeric vector... |
| make.abundancy.table | make.abundancy.table |
| matrix.padjust | matrix.padjust |
| microbiome-package | R package for microbiome studies |
| oligoTOhigher | oligo-species mappings |
| peerj32 | peerj32 data documentation |
| phylo.barplot | phylo.barplot |
| PhylotypeRatios | PhylotypeRatios |
| PlotBaggedRDA | Description: Bagged RDA visualization |
| plot_cumulative | plot_cumulative |
| polish.phylogeny.info | polish.phylogeny.info |
| prevalence | Simple prevalence measure |
| project.data | Project high-dimensional data on two-dimensional plane by... |
| read.profiling | read.profiling |
| relative.abundance | relative.abundance |
| retrieve.probesets | retrieve.probesets |
| roc | ROC analysis returning true and false positive rates along an... |
| roc.auc | ROC AUC calculation |
| roc.auc.matrix | ROC AUC calculation for a matrix of variables |
| roc.plot | Plot ROC curve |
| species2levels | Species-levels mappings |
| variability_individual | variability_individual |
