Package: granulator 1.15.0

Sabina Pfister

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:Sabina Pfister [aut, cre], Vincent Kuettel [aut], Enrico Ferrero [aut]

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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'))

Peer review:

Bug tracker:https://github.com/xanibas/granulator/issues

Datasets:

On BioConductor:granulator-1.15.0(bioc 3.21)granulator-1.14.0(bioc 3.20)

rnaseqgeneexpressiondifferentialexpressiontranscriptomicssinglecellstatisticalmethodregression

4.48 score 3 stars 6 scripts 258 downloads 12 exports 102 dependencies

Last updated 2 months agofrom:61e04a0f9e. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 24 2024
R-4.5-winOKNov 24 2024
R-4.5-linuxOKNov 24 2024
R-4.4-winOKNov 24 2024
R-4.4-macOKNov 24 2024
R-4.3-winOKNov 24 2024
R-4.3-macOKNov 24 2024

Exports:benchmarkcorrelatedeconvoluteget_decon_methodsget_TPMload_ABISplot_benchmarkplot_correlateplot_deconvoluteplot_proportionsplot_regressplot_similarity

Dependencies:askpassbase64encBiasedUrnbslibcachemclassclassIntclicolorspacecowplotcpp11data.tableDBIDEoptimRdigestdplyrdtanglee1071epiRevaluatefansifarverfastmapflextablefontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggplot2ggplotifygluegridGraphicsgtablehighrhtmltoolsisobandjquerylibjsonliteKernSmoothknitrlabelinglatticelifecyclelimSolvelpSolvelubridatemagrittrMASSMatrixmemoisemgcvmimemunsellnlmennlsofficeropensslpanderpheatmappillarpkgconfigproxypurrrquadprogR6raggrappdirsRColorBrewerRcpprlangrmarkdowns2sassscalessfstringistringrsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttimechangetinytexunitsutf8uuidvctrsviridisLitewithrwkxfunxml2yamlyulab.utilszipzoo

Deconvolution of bulk RNA-seq data with granulator

Rendered fromgranulator.Rmdusingknitr::rmarkdownon Nov 24 2024.

Last update: 2021-05-17
Started: 2021-05-03