Package: biomformat 1.41.0

Paul J. McMurdie

biomformat: An interface package for the BIOM file format

This is an R package for interfacing with the BIOM file format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.

Authors:Paul J. McMurdie [aut, cre], Joseph N. Paulson [aut]

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manual.pdf |manual.html✨
card.svg |card.png
biomformat/json (API)
NEWS

# Install 'biomformat' in R:
install.packages('biomformat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/joey711/biomformat/issues

On BioConductor:biomformat-1.41.0(bioc 3.24)biomformat-1.40.0(bioc 3.23)

immunooncologydataimportmetagenomicsmicrobiome

11.96 score 8 stars 49 packages 634 scripts 10k downloads 18 mentions 19 exports 3 dependencies

Last updated from:a7f85e0f54. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING215
linux-devel-x86_64NOTE281
source / vignettesOK210
linux-release-x86_64NOTE237
macos-release-arm64NOTE185
macos-oldrel-arm64NOTE206
windows-develNOTE203
windows-releaseNOTE194
windows-oldrelNOTE182
wasm-releaseOK139

Exports:as_tibble.biombiombiom_databiom_shapebiom_to_SummarizedExperimentcolnamesheadermake_biommatrix_element_typencolnrowobservation_metadataread_biomread_hdf5_biomrownamessample_metadatashowwrite_biomwrite_hdf5_biom

Dependencies:jsonlitelatticeMatrix

The biomformat package vignette

Paul J. McMurdie

Rendered frombiomformat.Rmdusingknitr::rmarkdownon Jun 09 2026.

Last update: 2026-03-15
Started: 2015-12-01

Readme and manuals

Help Manual

Help pageTopics
biomformat: An R interface to the BIOM file formatbiomformat-package biomformat
Coerce a biom object to a tidy tibbleas_tibble.biom
Coerce a biom object to a long-format tidy data frameas.data.frame.biom
Build and return an instance of the biom-class.biom biom,list-method
Access main data observation matrix data from 'biom-class'.biom_data biom_data,biom,ANY,character-method biom_data,biom,character,ANY-method biom_data,biom,character,missing-method biom_data,biom,missing,missing-method biom_data,biom,missing,numeric-method biom_data,biom,numeric,missing-method biom_data,biom,numeric,numeric-method
The matrix dimensions of a 'biom-class' object.biom_shape biom_shape,biom-method
Convert a biom object to a SummarizedExperimentbiom_to_SummarizedExperiment
The biom format data class.biom-class
Method extensions to 'colnames' for 'biom-class' objects.colnames,biom-method
Extract the header from a 'biom-class' object as a list.header header,biom-method
Create a 'biom-class' from 'matrix-class' or 'data.frame'.make_biom
Access class of data in the matrix elements of a 'biom-class' objectmatrix_element_type matrix_element_type,biom-method
Method extensions to 'ncol' for 'biom-class' objects.ncol,biom-method
Method extensions to 'nrow' for 'biom-class' objects.nrow,biom-method
Access observation (row) meta data from 'biom-class'.observation_metadata observation_metadata,biom,character-method observation_metadata,biom,missing-method observation_metadata,biom,numeric-method
Read a biom-format file, returning a 'biom-class'.read_biom
Read in a biom-format v2 (HDF5) file, returning a 'list'.read_hdf5_biom
Method extensions to 'rownames' for 'biom-class' objects.rownames,biom-method
Access meta data from 'biom-class'.sample_metadata sample_metadata,biom,character-method sample_metadata,biom,missing-method sample_metadata,biom,numeric-method
Method extensions to show for biom objects.show,biom-method
Write a biom-format v1 file, returning a 'biom-class'.write_biom
Write a biom object to an HDF5 (BIOM v2) file.write_hdf5_biom