Package: granulator 1.15.0
granulator: Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data
granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing interface to rapidly run and benchmark multiple state-of-the-art deconvolution methods. Data for the deconvolution of peripheral blood mononuclear cells (PBMCs) into individual immune cell types is provided as well.
Authors:
granulator_1.15.0.tar.gz
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granulator.pdf |granulator.html✨
granulator/json (API)
NEWS
# Install 'granulator' in R: |
install.packages('granulator', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/xanibas/granulator/issues
- bulkRNAseq_ABIS - PBMCs expression profiles
- groundTruth_ABIS - PBMCS true cell type proprotions
- sigMatrix_ABIS_S0 - Signature matrix for deconvolution of PBMCs in 17 cell types
- sigMatrix_ABIS_S1 - Signature matrix for deconvolution of PBMCs in 13 cell types
- sigMatrix_ABIS_S2 - Signature matrix for deconvolution of PBMCs in 11 cell types
- sigMatrix_ABIS_S3 - Signature matrix for deconvolution of PBMCs in 9 cell types
On BioConductor:granulator-1.15.0(bioc 3.21)granulator-1.14.0(bioc 3.20)
rnaseqgeneexpressiondifferentialexpressiontranscriptomicssinglecellstatisticalmethodregression
Last updated 2 months agofrom:61e04a0f9e. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 24 2024 |
R-4.5-win | OK | Nov 24 2024 |
R-4.5-linux | OK | Nov 24 2024 |
R-4.4-win | OK | Nov 24 2024 |
R-4.4-mac | OK | Nov 24 2024 |
R-4.3-win | OK | Nov 24 2024 |
R-4.3-mac | OK | Nov 24 2024 |
Exports:benchmarkcorrelatedeconvoluteget_decon_methodsget_TPMload_ABISplot_benchmarkplot_correlateplot_deconvoluteplot_proportionsplot_regressplot_similarity
Dependencies:askpassbase64encBiasedUrnbslibcachemclassclassIntclicolorspacecowplotcpp11data.tableDBIDEoptimRdigestdplyrdtanglee1071epiRevaluatefansifarverfastmapflextablefontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggplot2ggplotifygluegridGraphicsgtablehighrhtmltoolsisobandjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclelimSolvelpSolvelubridatemagrittrMASSMatrixmemoisemgcvmimemunsellnlmennlsofficeropensslpanderpheatmappillarpkgconfigproxypurrrquadprogR6raggrappdirsRColorBrewerRcpprlangrmarkdowns2sassscalessfstringistringrsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttimechangetinytexunitsutf8uuidvctrsviridisLitewithrwkxfunxml2yamlyulab.utilszipzoo