Introduction | Vignette Goals | Load data | Mosaic data integration with StabMap | Data imputation after StabMap | Annotating Query Datasets using the StabMap embedding | Indirect mosaic data integration with StabMap
Package: StabMap 1.7.0
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:
StabMap_1.7.0.tar.gz
StabMap_1.7.0.zip(r-4.7)StabMap_1.7.0.zip(r-4.6)StabMap_1.7.0.zip(r-4.5)
StabMap_1.7.0.tgz(r-4.6-any)StabMap_1.7.0.tgz(r-4.5-any)
StabMap_1.7.0.tar.gz(r-4.7-any)StabMap_1.7.0.tar.gz(r-4.6-any)
StabMap_1.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
StabMap/json (API)
| # Install 'StabMap' in R: |
| install.packages('StabMap', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sydneybiox/stabmap/issues
Pkgdown/docs site:https://sydneybiox.github.io
On BioConductor:StabMap-1.7.0(bioc 3.24)StabMap-1.6.0(bioc 3.23)
singlecelldimensionreductionsoftware
Last updated from:4cedc0ec96. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 217 | ||
| linux-devel-x86_64 | OK | 377 | ||
| source / vignettes | OK | 492 | ||
| linux-release-x86_64 | OK | 366 | ||
| macos-release-arm64 | OK | 173 | ||
| macos-oldrel-arm64 | OK | 168 | ||
| windows-devel | OK | 1251 | ||
| windows-release | OK | 1366 | ||
| windows-oldrel | OK | 1249 | ||
| wasm-release | OK | 190 |
Exports:adaptiveKNNclassifyEmbeddinggetAdaptiveKimputeEmbeddingmockMosaicDatamosaicDataTopologymosaicDataUpSetreWeightEmbeddingstabMap
Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularclicodetoolscpp11DelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomicRangesglueigraphIRangesirlbalambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatspkgconfigRcpprlangrsvdS4ArraysS4VectorsScaledMatrixSeqinfoslamsnowSparseArraySummarizedExperimentvctrsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Adaptive k-Nearest Neighbour Classification | adaptiveKNN |
| Adaptive k-Nearest Neighbour Classification using the StabMap joint embedding | classifyEmbedding |
| Adaptive k selection for KNN classification | getAdaptiveK |
| Impute values using StabMap joint embedding | imputeEmbedding |
| mockMosaicData | mockMosaicData |
| mosaicDataTopology | mosaicDataTopology |
| mosaicDataUpSet | mosaicDataUpSet |
| Re-weight StabMap embedding | reWeightEmbedding |
| Stabilised mosaic single cell data integration using unshared features | stabMap |
