biom: An interface package (beta) for the BIOM file format.

This is an R package for interfacing with the BIOM 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.

AuthorPaul J. McMurdie <mcmurdie@stanford.edu> and the biom-format team http://biom-format.org/
Date of publication2014-02-24 01:20:23
MaintainerPaul J. McMurdie <mcmurdie@stanford.edu>
LicenseGPL-2
Version0.3.12
https://github.com/joey711/biom/
http://biom-format.org/

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Files in this package

biom
biom/inst
biom/inst/tests
biom/inst/tests/test-accessors.R
biom/inst/tests/test-IO.R
biom/inst/NEWS
biom/inst/extdata
biom/inst/extdata/rich_dense_otu_table.biom
biom/inst/extdata/rich_dense_char.biom
biom/inst/extdata/rich_sparse_char.biom
biom/inst/extdata/min_sparse_otu_table.biom
biom/inst/extdata/rich_sparse_otu_table.biom
biom/inst/extdata/min_dense_otu_table.biom
biom/inst/doc
biom/inst/doc/biom-demo.R
biom/inst/doc/biom-demo.html
biom/inst/doc/placeholder.txt
biom/inst/doc/biom-demo.Rmd
biom/tests
biom/tests/testthat-biom.R
biom/NAMESPACE
biom/R
biom/R/BIOM-class.R biom/R/IO-methods.R biom/R/allClasses.R biom/R/allPackage.R biom/R/validity-methods.R
biom/vignettes
biom/vignettes/biom-demo.Rmd
biom/README.md
biom/MD5
biom/build
biom/build/vignette.rds
biom/DESCRIPTION
biom/man
biom/man/ncol-methods.Rd biom/man/read_biom.Rd biom/man/biom-package.Rd biom/man/biom-methods.Rd biom/man/biom_shape-methods.Rd biom/man/nrow-methods.Rd biom/man/biom-class.Rd biom/man/observation_metadata-methods.Rd biom/man/biom_data-methods.Rd biom/man/sample_metadata-methods.Rd biom/man/header-methods.Rd biom/man/colnames-methods.Rd biom/man/write_biom.Rd biom/man/rownames-methods.Rd biom/man/matrix_element_type-methods.Rd biom/man/show-methods.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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