Read/Write, Analyze, and Visualize 'BIOM' Data
Visualize alpha diversity with boxplots.
Visualize alpha diversity with scatterplots and trendlines.
Create a matrix of samples x alpha diversity metrics.
Test alpha diversity for associations with metadata.
Calculate the alpha diversity of each sample.
Convert a variety of data types to an rbiom object.
Convert an rbiom object to a base R list.
Convert an rbiom object to a simple count matrix.
Visualize BIOM data with boxplots.
Cluster samples by beta diversity k-means.
Visualize beta diversity with scatterplots and trendlines.
Display beta diversities in an all vs all grid.
Ordinate samples and taxa on a 2D plane based on beta diversity distan...
Calculate PCoA and other ordinations, including taxa biplots and stati...
Test beta diversity for associations with metadata.
Distance / dissimilarity between samples.
Apply a function to each subset of an rbiom object.
Combine several rbiom objects into one.
Convert biom data to an external package class.
Run ordinations on a distance matrix.
Run statistics on a distance matrix vs a categorical or numeric variab...
documentation_biom.rbiom
documentation_clusters
documentation_cmp
documentation_default
documentation_dist_test
documentation_heatmap
documentation_plot_return
documentation_rank.2
documentation_rank.NULL
documentation_return.biom
documentation_taxa.4
Export data to QIIME 2 or mothur.
Get a glimpse of your metadata.
Create, modify, and delete metadata fields.
Create a heatmap with tracks and dendrograms from any matrix.
Map sample names to metadata field values.
Visualize rarefaction curves with scatterplots and trendlines.
Combines rare_corrplot and rare_stacked into a single figure.
Visualize the number of observations per sample.
Transform a counts matrix.
Rarefy OTU counts.
Working with rbiom Objects.
Deprecated functions in package rbiom.
rbiom: Read/Write, Transform, and Summarize BIOM Data
Parse counts, metadata, taxonomy, and phylogeny from a BIOM file.
Parse a fasta file into a named character vector.
Read a newick formatted phylogenetic tree.
Objects exported from other packages
Summarize the taxa observations in each sample.
Subset to a specific number of samples.
Speed Ups.
Visualize categorical metadata effects on numeric values.
Visualize regression with scatterplots and trendlines.
Run non-parametric statistics on a data.frame.
Subset an rbiom object by sample names, OTU names, metadata, or taxono...
Visualize BIOM data with boxplots.
Cluster samples by taxa abundances k-means.
Visualize taxa abundance with scatterplots and trendlines.
Display taxa abundances as a heatmap.
Map OTUs names to taxa names at a given rank.
Taxa abundances per sample.
Display taxa abundances as a stacked bar graph.
Test taxa abundances for associations with metadata.
Get summary taxa abundances.
Create a subtree by specifying tips to keep.
Evaluate expressions on metadata.
Save an rbiom object to a file.
A toolkit for working with Biological Observation Matrix ('BIOM') files. Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and beta diversity (including 'UniFrac'). Summarize counts by taxonomic level. Subset based on metadata. Generate visualizations and statistical analyses. CPU intensive operations are coded in C for speed.
Useful links