Package: StabMap 1.1.0

Shila Ghazanfar

StabMap: Stabilised mosaic single cell data integration using unshared features

StabMap performs single cell mosaic data integration by first building a mosaic data topology, and for each reference dataset, traverses the topology to project and predict data onto a common embedding. Mosaic data should be provided in a list format, with all relevant features included in the data matrices within each list object. The output of stabMap is a joint low-dimensional embedding taking into account all available relevant features. Expression imputation can also be performed using the StabMap embedding and any of the original data matrices for given reference and query cell lists.

Authors:Shila Ghazanfar [aut, cre, ctb], Aiden Jin [ctb], Nicholas Robertson [ctb]

StabMap_1.1.0.tar.gz
StabMap_1.1.0.zip(r-4.5)StabMap_1.1.0.zip(r-4.4)StabMap_0.99.4.zip(r-4.3)
StabMap_1.1.0.tgz(r-4.4-any)StabMap_0.99.4.tgz(r-4.3-any)
StabMap_1.1.0.tar.gz(r-4.5-noble)StabMap_1.1.0.tar.gz(r-4.4-noble)
StabMap_1.1.0.tgz(r-4.4-emscripten)StabMap_0.99.4.tgz(r-4.3-emscripten)
StabMap.pdf |StabMap.html
StabMap/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/sydneybiox/stabmap/issues

On BioConductor:StabMap-1.1.0(bioc 3.21)StabMap-1.0.0(bioc 3.20)

singlecelldimensionreductionsoftware

6.03 score 60 scripts 9 exports 56 dependencies

Last updated 8 days agofrom:2005245e50. Checks:OK: 3 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxOKOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winWARNINGSep 07 2024
R-4.3-macWARNINGSep 07 2024

Exports:adaptiveKNNclassifyEmbeddinggetAdaptiveKimputeEmbeddingmockMosaicDatamosaicDataTopologymosaicDataUpSetreWeightEmbeddingstabMap

Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularclicodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrigraphIRangesirlbajsonlitelambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmimeopensslpkgconfigR6RcpprlangrsvdS4ArraysS4VectorsScaledMatrixslamsnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXVectorzlibbioc

StabMap: Stabilised mosaic single cell data integration using unshared features

Rendered fromstabMap_PBMC_Multiome.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-07-16
Started: 2023-11-28