Read/Write, Analyze, and Visualize 'BIOM' Data

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Documentation for package ‘rbiom’ version 2.0.10

Help Pages

adiv_boxplot Visualize alpha diversity with boxplots.
adiv_corrplot Visualize alpha diversity with scatterplots and trendlines.
adiv_matrix Create a matrix of samples x alpha diversity metrics.
adiv_stats Test alpha diversity for associations with metadata.
adiv_table Calculate the alpha diversity of each sample.
as.list.rbiom Convert an rbiom object to a base R list.
as.matrix.rbiom Convert an rbiom object to a simple count matrix.
as_rbiom Convert a variety of data types to an rbiom object.
babies Longitudinal Stool Samples from Infants (n = 2,684)
bdiv_boxplot Visualize BIOM data with boxplots.
bdiv_clusters Define sample PAM clusters from beta diversity.
bdiv_corrplot Visualize beta diversity with scatterplots and trendlines.
bdiv_distmat Distance / dissimilarity between samples.
bdiv_heatmap Display beta diversities in an all vs all grid.
bdiv_matrix Distance / dissimilarity between samples.
bdiv_ord_plot Ordinate samples and taxa on a 2D plane based on beta diversity distances.
bdiv_ord_table Calculate PCoA and other ordinations, including taxa biplots and statistics.
bdiv_stats Test beta diversity for associations with metadata.
bdiv_table Distance / dissimilarity between samples.
bdply Apply a function to each subset of an rbiom object.
biom_merge Combine several rbiom objects into one.
blply Apply a function to each subset of an rbiom object.
distmat_ord_table Run ordinations on a distance matrix.
distmat_stats Run statistics on a distance matrix vs a categorical or numeric variable.
gems Global Enteric Multicenter Study (n = 1,006)
glimpse.rbiom Get a glimpse of your metadata.
hmp50 Human Microbiome Project - demo dataset (n = 50)
modify_metadata Create, modify, and delete metadata fields.
mutate.rbiom Create, modify, and delete metadata fields.
na.omit.rbiom Subset an rbiom object by sample names, OTU names, metadata, or taxonomy.
plot_heatmap Create a heatmap with tracks and dendrograms from any matrix.
pull.rbiom Map sample names to metadata field values.
rarefy Rarefy OTU counts.
rarefy_cols Transform a counts matrix.
rare_corrplot Visualize rarefaction curves with scatterplots and trendlines.
rare_multiplot Combines rare_corrplot and rare_stacked into a single figure.
rare_stacked Visualize the number of observations per sample.
read_biom Parse counts, metadata, taxonomy, and phylogeny from a BIOM file.
read_fasta Parse a fasta file into a named character vector.
read_tree Read a newick formatted phylogenetic tree.
rename.rbiom Create, modify, and delete metadata fields.
rescale_cols Transform a counts matrix.
rescale_rows Transform a counts matrix.
sample_apply Summarize the taxa observations in each sample.
sample_sums Summarize the taxa observations in each sample.
slice.rbiom Subset to a specific number of samples.
slice_head.rbiom Subset to a specific number of samples.
slice_max.rbiom Subset to a specific number of samples.
slice_metadata Subset to a specific number of samples.
slice_min.rbiom Subset to a specific number of samples.
slice_sample.rbiom Subset to a specific number of samples.
slice_tail.rbiom Subset to a specific number of samples.
stats_boxplot Visualize categorical metadata effects on numeric values.
stats_corrplot Visualize regression with scatterplots and trendlines.
stats_table Run non-parametric statistics on a data.frame.
subset Subset an rbiom object by sample names, OTU names, metadata, or taxonomy.
subset.rbiom Subset an rbiom object by sample names, OTU names, metadata, or taxonomy.
subset_taxa Subset an rbiom object by sample names, OTU names, metadata, or taxonomy.
taxa_apply Get summary taxa abundances.
taxa_boxplot Visualize BIOM data with boxplots.
taxa_clusters Define sample kmeans clusters from taxa abundances.
taxa_corrplot Visualize taxa abundance with scatterplots and trendlines.
taxa_heatmap Display taxa abundances as a heatmap.
taxa_map Map OTUs names to taxa names at a given rank.
taxa_matrix Taxa abundances per sample.
taxa_means Get summary taxa abundances.
taxa_stacked Display taxa abundances as a stacked bar graph.
taxa_stats Test taxa abundances for associations with metadata.
taxa_sums Get summary taxa abundances.
taxa_table Taxa abundances per sample.
tree_subset Create a subtree by specifying tips to keep.
with Evaluate expressions on metadata.
with.rbiom Evaluate expressions on metadata.
within.rbiom Evaluate expressions on metadata.
write_biom Save an rbiom object to a file.
write_counts Save an rbiom object to a file.
write_fasta Save an rbiom object to a file.
write_metadata Save an rbiom object to a file.
write_taxonomy Save an rbiom object to a file.
write_tree Save an rbiom object to a file.
write_xlsx Save an rbiom object to a file.
[.rbiom Subset an rbiom object by sample names, OTU names, metadata, or taxonomy.