Man pages for MicrobiotaProcess
an R package for analysis, visualization and biomarker discovery of microbiome
| alphasample-class | alphasample class |
| as.data.frame | get the table of diffAnalysisClass |
| as.treedata | as.treedata |
| build_tree | building tree |
| clustplotClass-class | clustplotClass class |
| convert_to_treedata | convert dataframe contained hierarchical relationship or... |
| data-hmp_aerobiosis_small | (Data) Small subset of the HMP 16S dataset |
| data-kostic2012crc | (Data) Genomic analysis identifies association of... |
| data-test_otu_data | (Data) simulated dataset. |
| diff_analysis | Differential expression analysis |
| diffAnalysisClass-class | diffAnalysisClass class |
| drop_taxa | Dropping Species with Few abundance and Few Occurrences |
| generalizedFC | generalized fold change |
| get_alltaxadf | get the table of abundance of all level taxonomy |
| get_alphaindex | alpha index |
| get_clust | Hierarchical cluster analysis for the samples |
| get_coord | get ordination coordinates. |
| get_count | calculate the count or relative abundance of replicate... |
| get_dist | calculate distance |
| get_mean_median | get the mean and median of specific feature. |
| get_pca | Performs a principal components analysis |
| get_pcoa | performs principal coordinate analysis (PCoA) |
| get_pvalue | Methods for computation of the p-value |
| get_rarecurve | obtain the result of rare curve |
| get_sampledflist | Generate random data list from a original data. |
| get_taxadf | get the data of specified taxonomy |
| get_upset | generate the dataset for upset of UpSetR |
| get_varct | get the contribution of variables |
| get_vennlist | generate a vennlist for VennDiagram |
| ggbartax | taxonomy barplot |
| ggbox | A box or violin plot with significance test |
| ggclust | plot the result of hierarchical cluster analysis for the... |
| ggdiffbox | boxplot for the result of diff_analysis |
| ggdiffclade | plot the clade tree with highlight |
| ggdifftaxbar | significantly discriminative feature barplot |
| ggeffectsize | visualization of effect size by the Linear Discriminant... |
| ggordpoint | ordination plotter based on ggplot2. |
| ggrarecurve | Rarefaction alpha index |
| import_dada2 | Import function to load the feature table and taxanomy table... |
| import_qiime2 | Import function to load the output of qiime2. |
| multi_compare | a container for performing two or more sample test. |
| ordplotClass-class | ordplotClass class |
| pcasample-class | pcasample class |
| pcoa-class | pcoa class |
| prcomp-class | prcomp class |
| read_qza | read the qza file, output of qiime2. |
| reexports | Objects exported from other packages |
| show-methods | method extensions to show for diffAnalysisClass objects. |
| split_data | Split Large Vector or DataFrame |
| split_str_to_list | split a dataframe contained one column |
| theme_taxbar | theme_taxbar |
