Man pages for YuLab-SMU/MicrobiotaProcess
A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
| alphasample-class | alphasample class |
| as.MPSE | as.MPSE method |
| as.phyloseq | convert to phyloseq object. |
| as.treedata | as.treedata |
| build_tree | building tree |
| 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 |
| dr_extract | Extracting the internal tbl_df attribute of tibble. |
| drop_taxa | Dropping Species with Few abundance and Few Occurrences |
| extract_binary_offspring | extract the binary offspring of the specified internal nodes |
| 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_NRI_NTI-methods | calculating related phylogenetic alpha metric |
| 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 |
| ImportDada2 | Import function to load the feature table and taxonomy table... |
| ImportQiime2 | Import function to load the output of qiime2. |
| mouse.time.mpse | (Data) An example data |
| mp_adonis-methods | Permutational Multivariate Analysis of Variance Using... |
| mp_aggregate_clade-methods | calculate the mean/median (relative) abundance of internal... |
| mp_aggregate-methods | aggregate the assays with the specific group of sample and... |
| mp_anosim-methods | Analysis of Similarities (ANOSIM) with MPSE or tbl_mpse... |
| mp_balance_clade-methods | Calculating the balance score of internal nodes (clade)... |
| mp_cal_abundance-methods | Calculate the (relative) abundance of each taxonomy class for... |
| mp_cal_alpha-methods | calculate the alpha index with MPSE or tbl_mpse |
| mp_cal_cca-methods | [Partial] [Constrained] Correspondence Analysis with MPSE or... |
| mp_cal_clust-methods | Hierarchical cluster analysis for the samples with MPSE or... |
| mp_cal_dca-methods | Detrended Correspondence Analysis with MPSE or tbl_mpse... |
| mp_cal_dist-methods | Calculate the distances between the samples or features with... |
| mp_cal_divergence-methods | calculate the divergence with MPSE or tbl_mpse |
| mp_cal_nmds-methods | Nonmetric Multidimensional Scaling Analysis with MPSE or... |
| mp_cal_pca-methods | Principal Components Analysis with MPSE or tbl_mpse object |
| mp_cal_pcoa-methods | Principal Coordinate Analysis with MPSE or tbl_mpse object |
| mp_cal_pd_metric-methods | Calculating related phylogenetic alpha metric with MPSE or... |
| mp_cal_rarecurve-methods | Calculating the different alpha diversities index with... |
| mp_cal_rda-methods | [Partial] [Constrained] Redundancy Analysis with MPSE or... |
| mp_cal_upset-methods | Calculating the samples or groups for each OTU, the result... |
| mp_cal_venn-methods | Calculating the OTU for each sample or group, the result can... |
| mp_decostand-methods | This Function Provideds Several Standardization Methods for... |
| mp_diff_analysis-methods | Differential expression analysis for MPSE or tbl_mpse object |
| mp_diff_clade-methods | Differential internal and tip nodes (clades) analysis for... |
| mp_dmngroup-methods | Dirichlet-Multinomial generative classifiers to MPSE or... |
| mp_dmn-methods | Fit Dirichlet-Multinomial models to MPSE or tbl_mpse |
| mp_envfit-methods | Fits an Environmental Vector or Factor onto an Ordination... |
| mp_extract_abundance-methods | Extracting the abundance metric from MPSE or tbl_mpse object |
| mp_extract_assays-methods | extract the abundance matrix from MPSE object or tbl_mpse... |
| mp_extract_dist-methods | extract the dist object from MPSE or tbl_mpse object |
| mp_extract_feature-methods | extract the feature (OTU) information in MPSE object |
| mp_extract_internal_attr-methods | Extracting the PCA, PCoA, etc results from MPSE or tbl_mpse... |
| mp_extract_rarecurve-methods | Extract the result of mp_cal_rarecurve with action="add" from... |
| mp_extract_refseq-methods | Extract the representative sequences from MPSE object |
| mp_extract_sample-methods | extract the sample information in MPSE object |
| mp_extract_taxonomy-methods | extract the taxonomy annotation in MPSE object |
| mp_extract_tree-methods | extract the taxonomy tree in MPSE object |
| mp_filter_taxa-methods | Filter OTU (Features) By Abundance Level |
| mp_fortify | mp_fortify |
| mp_import_biom | building MPSE object from biom-format file. |
| mp_import_humann_regroup | Import function to load the output of human_regroup_table in... |
| mp_import_metaphlan | Import function to load the output of MetaPhlAn. |
| mp_import_qiime | Import function to load the output of qiime. |
| mp_mantel-methods | Mantel and Partial Mantel Tests for MPSE or tbl_mpse Object |
| mp_mrpp-methods | Analysis of Multi Response Permutation Procedure (MRPP) with... |
| mp_plot_abundance-methods | plotting the abundance of taxa via specified taxonomy class |
| mp_plot_alpha-methods | Plotting the alpha diversity between samples or groups. |
| mp_plot_diff_boxplot-methods | displaying the differential result contained abundance and... |
| mp_plot_diff_cladogram | Visualizing the result of mp_diff_analysis with cladogram. |
| mp_plot_diff_manhattan-methods | displaying the differential result contained abundance and... |
| mp_plot_diff_res-methods | The visualization of result of mp_diff_analysis |
| mp_plot_dist-methods | Plotting the distance between the samples with heatmap or... |
| mp_plot_ord-methods | Plotting the result of PCA, PCoA, CCA, RDA, NDMS or DCA |
| mp_plot_rarecurve-methods | Rarefaction alpha index with MPSE |
| mp_plot_upset-methods | Plotting the different number of OTU between group via UpSet... |
| mp_plot_venn-methods | Plotting the different number of OTU between groups with Venn... |
| mp_rrarefy-methods | mp_rrarefy method |
| MPSE | Construct a MPSE object |
| MPSE-accessors | MPSE accessors |
| MPSE-class | MPSE class |
| mp_select_as_tip-methods | select specific taxa level as rownames of MPSE |
| mp_stat_taxa-methods | Count the number and total number taxa for each sample at... |
| 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 |
| print some objects | |
| read_qza | read the qza file, output of qiime2. |
| reexports | Objects exported from other packages |
| scale_fill_diff_cladogram | Create the scale of mp_plot_diff_cladogram. |
| set_diff_boxplot_color | set the color scale of plot generated by mp_plot_diff_boxplot |
| set_scale_theme | adjust the color of heatmap of mp_plot_dist |
| show-methods | method extensions to show for diffAnalysisClass or... |
| split_data | Split Large Vector or DataFrame |
| split_str_to_list | split a dataframe contained one column |
| theme_taxbar | theme_taxbar |
