Skip to content
Tidy up computational biology objects
Branch: master
Clone or download
ajbass Merge pull request #18 from ltobalina/patch-1
Bugfix renaming of columns in augment.MArrayLM
Latest commit 3d7fa1d Aug 9, 2018
Type Name Latest commit message Commit time
Failed to load latest commit information.
R Bugfix renaming of columns in augment.MArrayLM Jul 30, 2018
data Initial commit. Tidying methods for ExpressionSet, edgeR, and limma c… Sep 23, 2014
tests Homogenizes output from tidiers and adds tests Nov 9, 2015
vignettes Update biobroom_vignette.Rmd Oct 21, 2015
NEWS Update Oct 21, 2015

Build Status biobroom: Tidying up computational biology

This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same the tidy/augment/glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.

biobroom implements tidying methods for both S3 and S4 classes. Objects that can be tidied include

  • ExpressionSet objects
  • RangedSummarizedExperiment objects
  • MSnSet objects
  • per-gene differential expression tests from limma, edgeR, and DESeq2
  • qvalue multiple hypothesis testing objects


The package can be installed with (requires devtools):


Find out more about the provided methods with:


Note on returned values

All biobroom tidy and augment methods, since they tend to be large data frames, return a tbl_df by default (this prevents them from printing many rows at once, while still acting like a traditional data.frame). To change this to a data.frame or data.table, you can set the biobroom.return option:

options(biobroom.return = "data.frame")
options(biobroom.return = "data.table")
You can’t perform that action at this time.