Package: CellScore 1.25.0
Nancy Mah
CellScore: Tool for Evaluation of Cell Identity from Transcription Profiles
The CellScore package contains functions to evaluate the cell identity of a test sample, given a cell transition defined with a starting (donor) cell type and a desired target cell type. The evaluation is based upon a scoring system, which uses a set of standard samples of known cell types, as the reference set. The functions have been carried out on a large set of microarray data from one platform (Affymetrix Human Genome U133 Plus 2.0). In principle, the method could be applied to any expression dataset, provided that there are a sufficient number of standard samples and that the data are normalized.
Authors:
CellScore_1.25.0.tar.gz
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CellScore.pdf |CellScore.html✨
CellScore/json (API)
| # Install 'CellScore' in R: |
| install.packages('CellScore', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:CellScore-1.25.0(bioc 3.20)CellScore-1.24.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:fc6e998b8b
Exports:BarplotOnOffBoxplotCellScoreCellScoreCellScoreReportCosineSimScoreextractTransitionsheatmapOnOffMarkersOnOffPcaStandardsPlotCosineSimHeatmapRugplotCellScorerugplotDonorTargetTestScatterplotCellScoreComponentsscatterplotDonorTargetTest
Dependencies:abindaskpassBiobaseBiocGenericsbitopscaToolscrayoncurlDelayedArrayGenomeInfoDbGenomeInfoDbDataGenomicRangesgplotsgtoolshttrIRangesjsonliteKernSmoothlatticelsaMatrixMatrixGenericsmatrixStatsmimeopensslR6RColorBrewerS4ArraysS4VectorsSnowballCSparseArraysquashSummarizedExperimentsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Pyramid barplot of on/off scores | BarplotOnOff |
| Boxplot of the CellScore values across test samples | BoxplotCellScore |
| CellScore evaluates the identity of cells undergoing cell type transition | CellScore |
| Generate a CellScore report | CellScoreReport |
| Cosine similarity score | CosineSimScore |
| Extract scores for given cell transitions | extractTransitions |
| heatmapOnOffMarkers | heatmapOnOffMarkers |
| On/off score | OnOff |
| PCA plot on the most variable portion of the standard expression dataset | PcaStandards |
| Plot heatmap of the cosine similarity score | PlotCosineSimHeatmap |
| RugplotCellScore | RugplotCellScore |
| rugplotDonorTargetTest | rugplotDonorTargetTest |
| Scatterplot of the the donor-like and target-like scores | ScatterplotCellScoreComponents |
| scatterplotDonorTargetTest | scatterplotDonorTargetTest |
