Package: biobroom 1.37.0

John D. Storey

biobroom: Turn Bioconductor objects into tidy data frames

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.

Authors:Andrew J. Bass, David G. Robinson, Steve Lianoglou, Emily Nelson, John D. Storey, with contributions from Laurent Gatto

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biobroom.pdf |biobroom.html✨
biobroom/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/storeylab/biobroom/issues

Datasets:
  • hammer - ExpressionSet results from Hammer et al 2010

On BioConductor:biobroom-1.37.0(bioc 3.20)biobroom-1.36.0(bioc 3.19)

bioconductor-package

27 exports 1.16 score 25 dependencies 1 dependents 1 mentions

Last updated 2 months agofrom:9ed01a1b69

Exports:augment_svaaugment.deSetaugment.DGEListaugment.MArrayLMaugment.qvalueglance_svaglance.deSetglance.DGEExactglance.GRangesglance.GRangesListglance.MArrayLMglance.qvaluetidy_svatidy.DESeqDataSettidy.DESeqResultstidy.deSettidy.DGEExacttidy.DGEListtidy.EListtidy.ExpressionSettidy.GRangestidy.GRangesListtidy.MAListtidy.MArrayLMtidy.MSnSettidy.qvaluetidy.RangedSummarizedExperiment

Dependencies:backportsBiobaseBiocGenericsbroomclicpp11dplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithr

biobroom Vignette

Andrew J. Bass, Emily Nelson, David Robinson and John D. Storey

Rendered frombiobroom_vignette.Rmdusingknitr::rmarkdownon Jun 17 2024.

Last update: 2018-08-30
Started: 2015-10-12

Readme and manuals

Help Manual

Help pageTopics
Tidying methods for a sva listaugment_sva glance_sva tidy_sva
Convert Bioconductor Object into Tidy Data Framesbiobroom-package biobroom
Tidying methods for DESeq2 DESeqDataSet objectsDESeq2_tidiers tidy.DESeqDataSet tidy.DESeqResults
Tidiers for edgeR's differential expression objectsaugment.DGEList edgeR_tidiers glance.DGEExact tidy.DGEExact tidy.DGEList
Tidying methods for Biobase's ExpressionSet objectsExpressionSet_tidiers tidy.ExpressionSet
ExpressionSet results from Hammer et al 2010hammer
Tidiers for the output of limma (linear models for microarray analysis)augment.MArrayLM glance.MArrayLM limma_tidiers tidy.EList tidy.MAList tidy.MArrayLM
Tidiers for return values from functions that aren't S3 objectsglance.list list_tidiers tidy.list
Tidying methods for Biobase's ExpressionSet objectsMSnSet_tidiers tidy.MSnSet
Tidying methods for a qvalue objectaugment.qvalue glance.qvalue qvalue_tidiers tidy.qvalue
Tidying methods for Biobase's SummarizedExperiment objectsSummarizedExperiment_tidiers tidy.RangedSummarizedExperiment
Tidying methods for edge's deSet objectaugment.deSet glance.deSet tidy.deSet
Tidying methods for GRanges and GRangesList objects.glance.GRanges glance.GRangesList tidy.GRanges tidy.GRangesList