Package: tiledbsoma 1.14.5

Aaron Wolen

tiledbsoma: 'TileDB' Stack of Matrices, Annotated ('SOMA')

Interface for working with 'TileDB'-based Stack of Matrices, Annotated ('SOMA'): an open data model for representing annotated matrices, like those commonly used for single cell data analysis. It is documented at <https://github.com/single-cell-data>; a formal specification available is at <https://github.com/single-cell-data/SOMA/blob/main/abstract_specification.md>.

Authors:Aaron Wolen [cre, aut], Dirk Eddelbuettel [aut], Paul Hoffman [aut], John Kerl [aut], TileDB, Inc. [cph, fnd]

tiledbsoma_1.14.5.tar.gz

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

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

Peer review:

Bug tracker:https://github.com/single-cell-data/tiledb-soma/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

9.23 score 90 stars 1 packages 24 scripts 70 exports 36 dependencies

Last updated 29 days agofrom:afca166d73 (on 1.14.5). Checks:OK: 1 WARNING: 5. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 23 2024
R-4.5-linux-x86_64WARNINGOct 23 2024
R-4.4-mac-x86_64WARNINGOct 23 2024
R-4.4-mac-aarch64WARNINGOct 23 2024
R-4.3-mac-x86_64WARNINGOct 23 2024
R-4.3-mac-aarch64WARNINGOct 23 2024

Exports:BlockwiseReadIterBaseBlockwiseSparseReadIterBlockwiseTableReadIterConfigListCoordsStriderdelete_metadataEphemeralCollectionEphemeralCollectionBaseEphemeralExperimentEphemeralMeasurementextract_datasetget_all_metadataget_metadataget_metadata_numhas_metadataIntIndexerlist_datasetsload_datasetMappingBasematrixZeroBasedViewPlatformConfigr_type_from_arrow_typeReadIterScalarMapset_log_levelset_metadatashow_package_versionssoma_contextSOMAAxisIndexerSOMAAxisQuerySOMAAxisQueryResultSOMACollectionSOMACollectionBaseSOMACollectionCreateSOMACollectionOpenSOMAContextBaseSOMADataFrameSOMADataFrameCreateSOMADataFrameOpenSOMADenseNDArraySOMADenseNDArrayCreateSOMADenseNDArrayOpenSOMAExperimentSOMAExperimentAxisQuerySOMAExperimentCreateSOMAExperimentOpenSOMAMeasurementSOMAMeasurementCreateSOMAMeasurementOpenSOMANDArrayBaseSOMAOpenSOMASparseNDArraySOMASparseNDArrayBlockwiseReadSOMASparseNDArrayCreateSOMASparseNDArrayOpenSOMASparseNDArrayReadSOMASparseNDArrayReadBaseSOMATileDBContextSparseReadIterTableReadIterTileDBArrayTileDBCreateOptionsTileDBGroupTileDBObjecttiledbsoma_stats_disabletiledbsoma_stats_dumptiledbsoma_stats_enabletiledbsoma_stats_resettiledbsoma_stats_showwrite_soma

Dependencies:arrowassertthatbitbit64clicpp11data.tablefansifsgluelatticelifecyclemagrittrMatrixnanoarrownanotimepillarpkgconfigpurrrR6RcppRcppCCTZRcppDateRcppInt64RcppSpdlogrlangspdltibbletidyselecttiledbtriebeardurltoolsutf8vctrswithrzoo

Querying a SOMA experiment

Rendered fromsoma-experiment-queries.Rmdusingknitr::rmarkdownon Oct 23 2024.

Last update: 2024-06-05
Started: 2023-05-05

Reading from SOMA objects

Rendered fromsoma-reading.Rmdusingknitr::rmarkdownon Oct 23 2024.

Last update: 2024-05-23
Started: 2023-05-05

SOMA objects overview

Rendered fromsoma-objects.Rmdusingknitr::rmarkdownon Oct 23 2024.

Last update: 2024-05-23
Started: 2023-05-05

Using PlatformConfig

Rendered fromUsingPlatformConfig.Rmdusingknitr::rmarkdownon Oct 23 2024.

Last update: 2023-04-10
Started: 2023-04-10

Readme and manuals

Help Manual

Help pageTopics
A Configuration ListConfigList
Delete metadata for given keydelete_metadata
SOMA Example Datasetsexample-datasets extract_dataset list_datasets load_dataset
Read all metadata (as named list)get_all_metadata
Read metadata (as a string)get_metadata
Get nnumber of metadata itemsget_metadata_num
Check for metadata given keyhas_metadata
The SOMA Re-IndexerIntIndexer
matrixZeroBasedView is a wrapper shim for a matrix or Matrix::sparseMatrix providingmatrixZeroBasedView
Platform ConfigurationPlatformConfig
Set the logging level for the R package and underlying C++ libraryset_log_level
Set metadata (as a string)set_metadata
Display package versionsshow_package_versions
Create and cache a SOMA Context Objectsoma_context
SOMA Axis QuerySOMAAxisQuery
'SOMAExperiment' Axis Query ResultSOMAAxisQueryResult
SOMA CollectionSOMACollection
Create SOMA CollectionSOMACollectionCreate
Open SOMA CollectionSOMACollectionOpen
SOMADataFrameSOMADataFrame
Create SOMA DataFrameSOMADataFrameCreate
Open SOMA DataFrameSOMADataFrameOpen
SOMADenseNDArraySOMADenseNDArray
Create SOMA Dense Nd ArraySOMADenseNDArrayCreate
Open SOMA Dense Nd ArraySOMADenseNDArrayOpen
SOMA ExperimentSOMAExperiment
'SOMAExperiment' Axis QuerySOMAExperimentAxisQuery
Create SOMA ExperimentSOMAExperimentCreate
Open SOMA ExperimentSOMAExperimentOpen
SOMA MeasurementSOMAMeasurement
Create SOMA MeasurementSOMAMeasurementCreate
Open SOMA MeasurementSOMAMeasurementOpen
Open a SOMA ObjectSOMAOpen
SOMASparseNDArraySOMASparseNDArray
Create SOMA Sparse Nd ArraySOMASparseNDArrayCreate
Open SOMA Sparse Nd ArraySOMASparseNDArrayOpen
SOMA TileDB ContextSOMATileDBContext
SparseReadIterSparseReadIter
SOMA Read Iterator over Arrow TableTableReadIter
TileDB Object Base ClassTileDBObject
TileDB SOMA statisticstiledbsoma_stats tiledbsoma_stats_disable tiledbsoma_stats_dump tiledbsoma_stats_enable tiledbsoma_stats_reset tiledbsoma_stats_show
Write a SOMA Object from an R Objectwrite_soma
Write a 'Seurat' object to a SOMAwrite_soma.Seurat
Write a 'SingleCellExperiment' object to a SOMAwrite_soma.SingleCellExperiment
Write a 'SummarizedExperiment' object to a SOMAwrite_soma.SummarizedExperiment