Package: tidySummarizedExperiment 1.23.0

Stefano Mangiola

tidySummarizedExperiment: Brings SummarizedExperiment to the Tidyverse

The tidySummarizedExperiment package provides a set of tools for creating and manipulating tidy data representations of SummarizedExperiment objects. SummarizedExperiment is a widely used data structure in bioinformatics for storing high-throughput genomic data, such as gene expression or DNA sequencing data. The tidySummarizedExperiment package introduces a tidy framework for working with SummarizedExperiment objects. It allows users to convert their data into a tidy format, where each observation is a row and each variable is a column. This tidy representation simplifies data manipulation, integration with other tidyverse packages, and enables seamless integration with the broader ecosystem of tidy tools for data analysis.

Authors:Stefano Mangiola [aut, cre] <[email protected]>

# Install 'tidySummarizedExperiment' in R:

install.packages('tidySummarizedExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/stemangiola/tidysummarizedexperiment/issues

Datasets:

pasilla - Read counts of RNA-seq samples of Pasilla knock-down by Brooks et al.
se - Read counts of RNA-seq samples derived from Pasilla knock-down by Brooks et al.

On BioConductor:tidySummarizedExperiment-1.23.0(bioc 3.24)tidySummarizedExperiment-1.22.0(bioc 3.23)

assaydomain infrastructure rnaseq differentialexpression geneexpression normalization clustering qualitycontrol sequencing transcription transcriptomics bioconductor genomics summarizedexperiment tidyverse

8.98 score 30 stars 1 packages 350 scripts 3 exports 84 dependencies

Last updated from:c35aee3b73. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	224
linux-devel-x86_64	NOTE	432
source / vignettes	OK	256
linux-release-x86_64	NOTE	430
macos-release-arm64	NOTE	214
macos-oldrel-arm64	NOTE	227
windows-devel	NOTE	299
windows-release	NOTE	291
windows-oldrel	NOTE	322
wasm-release	OK	174

Exports:%>%tidy unnest_summarized_experiment

Dependencies:abind askpass base64enc Biobase BiocGenerics bslib cachem cli cpp11 crosstalk curl data.table DelayedArray digest dplyr ellipsis evaluate fansi farver fastmap fontawesome fs generics GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl otel pillar pkgconfig plotly plyxp promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S4Arrays S4Vectors S7 sass scales Seqinfo SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex ttservice utf8 vctrs viridisLite withr xfun XVector yaml

Overview of the tidySummarizedExperiment package

Rendered fromintroduction.Rmdusingknitr::knitr

Last update: 2025-10-12
Started: 2020-09-09

Help page	Topics
Append samples from multiple SummarizedExperiment objects	append_samples append_samples.SummarizedExperiment
Coerce lists, matrices, and more to data frames	as_tibble as_tibble.SummarizedExperiment
Efficiently bind multiple data frames by row and column	bind_cols bind_cols.RangedSummarizedExperiment bind_cols.SummarizedExperiment bind_rows bind_rows.SummarizedExperiment
Count the observations in each group	count count.SummarizedExperiment
Keep distinct/unique rows	distinct distinct.SummarizedExperiment
Extract a character column into multiple columns using regular expression groups	extract extract.SummarizedExperiment
Keep rows that match a condition	filter filter.SummarizedExperiment
Mutating joins	full_join full_join.SummarizedExperiment
Create a new 'ggplot' from a 'SummarizedExperiment'	ggplot ggplot.SummarizedExperiment
Group by one or more variables	group_by group_by.SummarizedExperiment
Split data frame by groups	group_split group_split.SummarizedExperiment
Mutating joins	inner_join inner_join.SummarizedExperiment
Mutating joins	left_join left_join.SummarizedExperiment
Create, modify, and delete columns	mutate mutate.SummarizedExperiment
Nest rows into a list-column of data frames	nest nest.SummarizedExperiment
Read counts of RNA-seq samples of Pasilla knock-down by Brooks et al.	pasilla
Pivot data from wide to long	pivot_longer pivot_longer.SummarizedExperiment
Pivot data from long to wide	pivot_wider pivot_wider.SummarizedExperiment
Initiate a plotly visualization	plot_ly plot_ly.SummarizedExperiment plot_ly.tbl_df
Extract a single column	pull pull.SummarizedExperiment
Rename columns	rename rename.SummarizedExperiment
Mutating joins	right_join right_join.SummarizedExperiment
Group input by rows	rowwise rowwise.SummarizedExperiment
Sample n rows from a table	sample_frac sample_frac.SummarizedExperiment sample_n sample_n.SummarizedExperiment
Read counts of RNA-seq samples derived from Pasilla knock-down by Brooks et al.	se
Keep or drop columns using their names and types	select select.SummarizedExperiment
Separate a character column into multiple columns with a regular expression or numeric locations	separate separate.SummarizedExperiment
Subset rows using their positions	slice slice.SummarizedExperiment slice_head slice_max slice_min slice_sample slice_tail
Summarise each group down to one row	summarise summarise.SummarizedExperiment summarize summarize.SummarizedExperiment
tidy for 'Seurat'	tidy tidy.RangedSummarizedExperiment tidy.SummarizedExperiment
Unite multiple columns into one by pasting strings together	unite unite.SummarizedExperiment
Unnest a list-column of data frames into rows and columns	unnest unnest.tidySummarizedExperiment_nested unnest_summarized_experiment

Package: tidySummarizedExperiment 1.23.0

tidySummarizedExperiment: Brings SummarizedExperiment to the Tidyverse

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