Package: tidySummarizedExperiment 1.17.0
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:
tidySummarizedExperiment_1.17.0.tar.gz
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tidySummarizedExperiment.pdf |tidySummarizedExperiment.html✨
tidySummarizedExperiment/json (API)
| # 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
On BioConductor:tidySummarizedExperiment-1.17.0(bioc 3.21)tidySummarizedExperiment-1.16.0(bioc 3.20)
assaydomaininfrastructurernaseqdifferentialexpressiongeneexpressionnormalizationclusteringqualitycontrolsequencingtranscriptiontranscriptomics
Last updated 2 months agofrom:84d246be81. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win | NOTE | Dec 18 2024 |
| R-4.5-linux | NOTE | Dec 18 2024 |
| R-4.4-win | NOTE | Dec 18 2024 |
| R-4.4-mac | NOTE | Dec 18 2024 |
| R-4.3-win | NOTE | Dec 18 2024 |
| R-4.3-mac | NOTE | Dec 18 2024 |
Exports:%>%mutate_featuresmutate_samplestidyunnest_summarized_experiment
Dependencies:abindaskpassbase64encBiobaseBiocGenericsbslibcachemclicolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdplyrellipsisevaluatefansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownS4ArraysS4VectorssassscalesSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexttserviceUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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 |
| Printing tibbles | formatting print print.SummarizedExperiment |
| Mutating joins | full_join full_join.SummarizedExperiment |
| Create a new 'ggplot' from a 'tidyseurat' | 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 |
| Mutate features | mutate_features |
| Mutate samples | mutate_samples |
| 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 |
| Format the header of a tibble | tbl_format_header tbl_format_header.tidySummarizedExperiment |
| 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 |
