Introduction | Installation | Data representation of tidySingleCellExperiment | Annotation polishing | Preliminary plots | Preprocessing | Clustering | Combining datasets | Reduce dimensions | Cell type prediction | Nested analyses | Aggregating cells | Session Info | References
Package: tidySingleCellExperiment 1.23.0
Stefano Mangiola
tidySingleCellExperiment: Brings SingleCellExperiment to the Tidyverse
'tidySingleCellExperiment' is an adapter that abstracts the 'SingleCellExperiment' container in the form of a 'tibble'. This allows *tidy* data manipulation, nesting, and plotting. For example, a 'tidySingleCellExperiment' is directly compatible with functions from 'tidyverse' packages `dplyr` and `tidyr`, as well as plotting with `ggplot2` and `plotly`. In addition, the package provides various utility functions specific to single-cell omics data analysis (e.g., aggregation of cell-level data to pseudobulks).
Authors:
tidySingleCellExperiment_1.23.0.tar.gz
tidySingleCellExperiment_1.23.0.zip(r-4.7)tidySingleCellExperiment_1.23.0.zip(r-4.6)tidySingleCellExperiment_1.23.0.zip(r-4.5)
tidySingleCellExperiment_1.23.0.tgz(r-4.6-any)tidySingleCellExperiment_1.23.0.tgz(r-4.5-any)
tidySingleCellExperiment_1.23.0.tar.gz(r-4.7-any)tidySingleCellExperiment_1.23.0.tar.gz(r-4.6-any)
tidySingleCellExperiment_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
tidySingleCellExperiment/json (API)
| # Install 'tidySingleCellExperiment' in R: |
| install.packages('tidySingleCellExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/stemangiola/tidysinglecellexperiment/issues
Datasets:
- cell_type_df - Cell types of 80 PBMC single cells
- pbmc_small - Pbmc_small
- pbmc_small_nested_interactions - Intercellular ligand-receptor interactions for 38 ligands from a single cell RNA-seq cluster.
On BioConductor:tidySingleCellExperiment-1.23.0(bioc 3.24)tidySingleCellExperiment-1.22.0(bioc 3.23)
assaydomaininfrastructurernaseqdifferentialexpressionsinglecellgeneexpressionnormalizationclusteringqualitycontrolsequencingbioconductordplyrggplot2plotlysingle-cell-rna-seqsingle-cell-sequencingsinglecellexperimenttibbletidyrtidyverse
Last updated from:6e9b8875cf. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 272 | ||
| linux-devel-x86_64 | OK | 451 | ||
| source / vignettes | OK | 423 | ||
| linux-release-x86_64 | OK | 435 | ||
| macos-release-arm64 | OK | 210 | ||
| macos-oldrel-arm64 | OK | 190 | ||
| windows-devel | OK | 832 | ||
| windows-release | OK | 1262 | ||
| windows-oldrel | OK | 1189 | ||
| wasm-release | OK | 271 |
Exports:%>%aggregate_cellsjoin_featuresjoin_transcriptstidyunnest_single_cell_experiment
Dependencies:abindaskpassbase64encBiobaseBiocGenericsbslibcachemclicpp11crosstalkcurldata.tableDelayedArraydigestdplyrellipsisevaluatefansifarverfastmapfontawesomefsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoSingleCellExperimentSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexttserviceutf8vctrsviridisLitewithrxfunXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Aggregate cells | aggregate_cells aggregate_cells,SingleCellExperiment-method |
| Filtering joins | anti_join anti_join.SingleCellExperiment |
| Append samples from multiple SingleCellExperiment objects | append_samples append_samples.SingleCellExperiment |
| Order rows using column values | arrange arrange.SingleCellExperiment |
| Coerce lists, matrices, and more to data frames | as_tibble as_tibble.SingleCellExperiment |
| Cell types of 80 PBMC single cells | cell_type_df |
| Count the observations in each group | add_count add_count.SingleCellExperiment count count.SingleCellExperiment |
| Keep distinct/unique rows | distinct distinct.SingleCellExperiment |
| Extract a character column into multiple columns using regular expression groups | extract extract.SingleCellExperiment |
| Keep rows that match a condition | filter filter.SingleCellExperiment |
| Printing tibbles | formatting print print.SingleCellExperiment |
| Mutating joins | full_join full_join.SingleCellExperiment |
| Create a new 'ggplot' from a 'tidySingleCellExperiment' | ggplot ggplot.SingleCellExperiment |
| Get a glimpse of your data | glimpse glimpse.tidySingleCellExperiment |
| Group by one or more variables | group_by group_by.SingleCellExperiment |
| Split data frame by groups | group_split group_split.SingleCellExperiment |
| Mutating joins | inner_join inner_join.SingleCellExperiment |
| join_features | join_features join_features,SingleCellExperiment-method |
| (DEPRECATED) Extract and join information for transcripts. | join_transcripts |
| Mutating joins | left_join left_join.SingleCellExperiment |
| Create, modify, and delete columns | mutate mutate.SingleCellExperiment |
| Nest rows into a list-column of data frames | nest nest.SingleCellExperiment |
| pbmc_small | pbmc_small |
| Intercellular ligand-receptor interactions for 38 ligands from a single cell RNA-seq cluster. | pbmc_small_nested_interactions |
| Pivot data from wide to long | pivot_longer pivot_longer.SingleCellExperiment |
| Initiate a plotly visualization | plot_ly plot_ly.SingleCellExperiment |
| Extract a single column | pull pull.SingleCellExperiment |
| Rename columns | rename rename.SingleCellExperiment |
| returns variables from an expression | return_arguments_of |
| Mutating joins | right_join right_join.SingleCellExperiment |
| Group input by rows | rowwise rowwise.SingleCellExperiment |
| Sample n rows from a table | sample_frac sample_frac.SingleCellExperiment sample_n sample_n.SingleCellExperiment |
| Keep or drop columns using their names and types | select select.SingleCellExperiment |
| Separate a character column into multiple columns with a regular expression or numeric locations | separate separate.SingleCellExperiment |
| Subset rows using their positions | slice slice.SingleCellExperiment slice_head slice_head.SingleCellExperiment slice_max slice_max.SingleCellExperiment slice_min slice_min.SingleCellExperiment slice_sample slice_sample.SingleCellExperiment slice_tail slice_tail.SingleCellExperiment |
| Summarise each group down to one row | summarise summarise.SingleCellExperiment summarize summarize.SingleCellExperiment |
| Format the header of a tibble | tbl_format_header tbl_format_header.tidySingleCellExperiment |
| (DEPRECATED) tidy for `SingleCellExperiment` | tidy tidy.SingleCellExperiment |
| Unite multiple columns into one by pasting strings together | unite unite.SingleCellExperiment |
| Unnest a list-column of data frames into rows and columns | unnest unnest.tidySingleCellExperiment_nested unnest_single_cell_experiment |
