biobroom: Turn Bioconductor objects into tidy data frames

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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.

Author
Andrew J. Bass, David G. Robinson, Steve Lianoglou, Emily Nelson, John D. Storey, with contributions from Laurent Gatto
Date of publication
None
Maintainer
John D. Storey <jstorey@princeton.edu> and Andrew J. Bass <ajbass@princeton.edu>
License
LGPL
Version
1.6.0
URLs

View on Bioconductor

Man pages

biobroom
Convert Bioconductor Object into Tidy Data Frames
DESeq2_tidiers
Tidying methods for DESeq2 DESeqDataSet objects
edgeR_tidiers
Tidiers for edgeR's differential expression objects
edge_tidiers
Tidying methods for edge's deSet object
ExpressionSet_tidiers
Tidying methods for Biobase's ExpressionSet objects
GRanges_tidiers
Tidying methods for GRanges and GRangesList objects.
hammer
ExpressionSet results from Hammer et al 2010
limma_tidiers
Tidiers for the output of limma (linear models for microarray...
list_tidiers
Tidiers for return values from functions that aren't S3...
MSnSet_tidiers
Tidying methods for Biobase's ExpressionSet objects
qvalue_tidiers
Tidying methods for a qvalue object
SummarizedExperiment_tidiers
Tidying methods for Biobase's SummarizedExperiment objects
sva_tidiers
Tidying methods for a sva list

Files in this package

biobroom/DESCRIPTION
biobroom/NAMESPACE
biobroom/NEWS
biobroom/R
biobroom/R/DESeq2_tidiers.R
biobroom/R/ExpressionSet_tidiers.R
biobroom/R/GRanges_tidiers.R
biobroom/R/MSnSet_tidiers.R
biobroom/R/SummarizedExperiment_tidiers.R
biobroom/R/biobroom.R
biobroom/R/edgeR_tidiers.R
biobroom/R/edge_tidiers.R
biobroom/R/hammer-data.R
biobroom/R/limma_tidiers.R
biobroom/R/list_tidiers.R
biobroom/R/qvalue_tidiers.R
biobroom/R/sva_tidiers.R
biobroom/R/testing_helpers.R
biobroom/R/utilities.R
biobroom/README.md
biobroom/build
biobroom/build/vignette.rds
biobroom/data
biobroom/data/hammer.rda
biobroom/inst
biobroom/inst/doc
biobroom/inst/doc/biobroom_vignette.R
biobroom/inst/doc/biobroom_vignette.Rmd
biobroom/inst/doc/biobroom_vignette.html
biobroom/man
biobroom/man/DESeq2_tidiers.Rd
biobroom/man/ExpressionSet_tidiers.Rd
biobroom/man/GRanges_tidiers.Rd
biobroom/man/MSnSet_tidiers.Rd
biobroom/man/SummarizedExperiment_tidiers.Rd
biobroom/man/biobroom.Rd
biobroom/man/edgeR_tidiers.Rd
biobroom/man/edge_tidiers.Rd
biobroom/man/hammer.Rd
biobroom/man/limma_tidiers.Rd
biobroom/man/list_tidiers.Rd
biobroom/man/qvalue_tidiers.Rd
biobroom/man/sva_tidiers.Rd
biobroom/tests
biobroom/tests/testthat
biobroom/tests/testthat.R
biobroom/tests/testthat/test-DESeq2_tidiers.R
biobroom/tests/testthat/test-ExpressionSet.R
biobroom/tests/testthat/test-edgeR_tidiers.R
biobroom/tests/testthat/test-limma_tidiers.R
biobroom/tests/testthat/test-testing_helpers.R
biobroom/vignettes
biobroom/vignettes/biobroom_vignette.Rmd