Package: tiledbsoma 2.3.0

Paul Hoffman

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:Paul Hoffman [cre, aut], Aaron Wolen [aut], Julia Dark [ctb], John Kerl [ctb], TileDB, Inc. [cph, fnd]

tiledbsoma_2.3.0.tar.gz

tiledbsoma_2.3.0.tgz(r-4.6-x86_64)tiledbsoma_2.3.0.tgz(r-4.6-arm64)tiledbsoma_2.3.0.tgz(r-4.5-x86_64)tiledbsoma_2.3.0.tgz(r-4.5-arm64)
tiledbsoma_2.3.0.tar.gz(r-4.7-x86_64)tiledbsoma_2.3.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
tiledbsoma/json (API)
NEWS

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

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

Pkgdown/docs site:https://single-cell-data.github.io

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

On CRAN:

Conda:

single-cellsingle-cell-genomicstiledbtiledb-apitiledb-somacpp

9.66 score 126 stars 1 packages 58 scripts 65 exports 29 dependencies

Last updated from:aac88138d1 (on 2.3.0). Checks:3 FAIL, 3 WARNING, 7 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64FAIL423
linux-devel-x86_64WARNING1028
source / vignettesOK1463
linux-release-arm64FAIL451
linux-release-x86_64WARNING947
macos-release-arm64WARNING334
macos-release-x86_64OK782
macos-oldrel-arm64OK422
macos-oldrel-x86_64OK945
windows-develOK224
windows-releaseOK172
windows-oldrelOK173
wasm-releaseFAIL175

Exports:BlockwiseReadIterBaseBlockwiseSparseReadIterBlockwiseTableReadIterConfigListCoordsStriderEphemeralCollectionEphemeralCollectionBaseEphemeralExperimentEphemeralMeasurementextract_datasetget_default_contextIntIndexerlist_datasetsload_datasetMappingBasematrixZeroBasedViewPlatformConfigReadIterScalarMapset_default_contextset_log_levelshow_package_versionssoma_contextSOMAArrayBaseSOMAAxisIndexerSOMAAxisQuerySOMAAxisQueryResultSOMACollectionSOMACollectionBaseSOMACollectionCreateSOMACollectionOpenSOMAContextSOMAContextBaseSOMADataFrameSOMADataFrameCreateSOMADataFrameOpenSOMADenseNDArraySOMADenseNDArrayCreateSOMADenseNDArrayOpenSOMAExperimentSOMAExperimentAxisQuerySOMAExperimentCreateSOMAExperimentOpenSOMAMeasurementSOMAMeasurementCreateSOMAMeasurementOpenSOMANDArrayBaseSOMAObjectSOMAOpenSOMASparseNDArraySOMASparseNDArrayBlockwiseReadSOMASparseNDArrayCreateSOMASparseNDArrayOpenSOMASparseNDArrayReadSOMASparseNDArrayReadBaseSOMATileDBContextSparseReadIterTableReadIterTileDBCreateOptionstiledbsoma_stats_disabletiledbsoma_stats_dumptiledbsoma_stats_enabletiledbsoma_stats_resettiledbsoma_stats_showwrite_soma

Dependencies:arrowassertthatbitbit64clicpp11data.tablefsgluelatticelifecyclemagrittrMatrixnanoarrownanotimepurrrR6RcppRcppCCTZRcppDateRcppInt64RcppSpdlogrlangspdltidyselecttiledbvctrswithrzoo

Querying a SOMA experiment

Rendered fromsoma-experiment-queries.Rmdusingknitr::rmarkdownon May 27 2026.

Last update: 2025-05-13
Started: 2023-05-05

Reading from SOMA objects

Rendered fromsoma-reading.Rmdusingknitr::rmarkdownon May 27 2026.

Last update: 2025-05-13
Started: 2023-05-05

SOMA objects overview

Rendered fromsoma-objects.Rmdusingknitr::rmarkdownon May 27 2026.

Last update: 2025-05-13
Started: 2023-05-05

SOMA shapes

Rendered fromsoma-shapes.Rmdusingknitr::rmarkdownon May 27 2026.

Last update: 2025-05-13
Started: 2024-12-04

Using PlatformConfig

Rendered fromUsingPlatformConfig.Rmdusingknitr::rmarkdownon May 27 2026.

Last update: 2025-05-13
Started: 2023-04-10

Readme and manuals

Help Manual

Help pageTopics
A Configuration ListConfigList
SOMA Example Datasetsexample-datasets extract_dataset list_datasets load_dataset
Get the Default SOMA Contextget_default_context
The SOMA Re-IndexerIntIndexer
Zero-based Wrapper for Sparse MatricesmatrixZeroBasedView
Platform ConfigurationPlatformConfig
Set the Default Global Contextset_default_context
Set TileDB-SOMA Logging Levelset_log_level
Display package versionsshow_package_versions
SOMA Axis QuerySOMAAxisQuery
'SOMAExperiment' Axis Query ResultSOMAAxisQueryResult
SOMA CollectionSOMACollection
Create a SOMA CollectionSOMACollectionCreate
Open a SOMA CollectionSOMACollectionOpen
SOMA ContextSOMAContext
SOMADataFrameSOMADataFrame
Create a SOMA Data FrameSOMADataFrameCreate
Open a SOMA Data FrameSOMADataFrameOpen
SOMA Dense Nd-ArraySOMADenseNDArray
Create a SOMA Dense ND ArraySOMADenseNDArrayCreate
Open a SOMA Dense Nd ArraySOMADenseNDArrayOpen
SOMA ExperimentSOMAExperiment
'SOMAExperiment' Axis QuerySOMAExperimentAxisQuery
Create a SOMA ExperimentSOMAExperimentCreate
Open SOMA ExperimentSOMAExperimentOpen
SOMA MeasurementSOMAMeasurement
Create a SOMA MeasurementSOMAMeasurementCreate
Open SOMA MeasurementSOMAMeasurementOpen
Open a SOMA ObjectSOMAOpen
SOMA Sparse Nd-ArraySOMASparseNDArray
Create a SOMA Sparse ND ArraySOMASparseNDArrayCreate
Open a SOMA Sparse ND ArraySOMASparseNDArrayOpen
SOMA TileDB ContextSOMATileDBContext
SOMA Read Iterator Over Sparse MatricesSparseReadIter
SOMA Read Iterator Over Arrow TablesTableReadIter
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