Man pages for rbiom
Read/Write, Transform, and Summarize 'BIOM' Data

alpha.divEstimate the diversity of each sample.
beta.divMake a distance matrix of samples vs samples.
countsGet the abundance counts.
infoGet biom's misc information.
metadataGet the sample metadata.
nsamplesNumber of samples in a BIOM.
ntaxaNumber of taxa in a BIOM.
phylogenyGet the phylogenetic tree.
pipePipe operator
printSummarize the contents of a BIOM object
rarefySubset counts so that all samples have the same number of...
rbiomrbiom: Read/Write, Transform, and Summarize BIOM Data
read.biomExtracts counts, metadata, taxonomy, and phylogeny from a...
read.fastaParse a fasta file into a named character vector.
read.treeRead a newick formatted phylogenetic tree.
sample.namesGet the sample names.
selectReduce samples to a specific list
sequencesDNA sequence associated with each taxonomic identifier.
subsetSubset samples using the BIOM object's metadata
subtreeCreate a subtree by specifying tips to keep.
taxa.namesGet the taxa names.
taxa.ranksGet the taxa ranks.
taxa.rollupGenerate a matrix of samples by taxa, at the specified...
taxonomyGet the taxonomy table.
tipsNames of a phylogenetic tree's tips/leafs.
unifracCompute Weighted and Unweighted UniFrac distance matrices.
write.biomWrite counts, metadata, taxonomy, and phylogeny to a biom...
write.fastaWrite sequences from a BIOM object to a file in fasta format.
write.treeWrite a newick formatted phylogenetic tree.
write.xlsxWrite data and summary information to a Microsoft...
rbiom documentation built on Nov. 5, 2021, 9:11 a.m.