Package: granulator 1.20.0

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]

granulator_1.20.0.tar.gz
granulator_1.20.0.zip(r-4.7-any)granulator_1.20.0.zip(r-4.6-any)granulator_1.20.0.zip(r-4.5-any)
granulator_1.20.0.tgz(r-4.6-any)granulator_1.20.0.tgz(r-4.5-any)
granulator_1.20.0.tar.gz(r-4.7-any)granulator_1.20.0.tar.gz(r-4.6-any)
granulator_1.20.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
granulator/json (API)

# Install 'granulator' in R:

install.packages('granulator', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

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

Datasets:

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 CRAN:

rnaseq geneexpression differentialexpression transcriptomics singlecell statisticalmethod regression

3.98 score 3 stars 21 scripts 230 downloads 12 exports 98 dependencies

Last updated from:b87f30eb2f (on RELEASE_3_23). Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	170
linux-devel-x86_64	ERROR	422
source / vignettes	OK	331
linux-release-x86_64	ERROR	530
macos-release-arm64	ERROR	302
macos-oldrel-arm64	ERROR	319
windows-devel	ERROR	369
windows-release	ERROR	311
windows-oldrel	ERROR	441
wasm-release	OK	172

Exports:benchmark correlate deconvolute get_decon_methods get_TPM load_ABIS plot_benchmark plot_correlate plot_deconvolute plot_proportions plot_regress plot_similarity

Dependencies:askpass base64enc BiasedUrn bslib cachem class classInt cli cowplot cpp11 data.table DBI DEoptimR digest dplyr dtangle e1071 epiR evaluate farver fastmap flextable fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics ggplot2 ggplotify glue gridGraphics gtable highr htmltools isoband jquerylib jsonlite KernSmooth knitr labeling lattice lifecycle limSolve lpSolve lubridate magrittr MASS Matrix memoise mime nnls officer openssl pander pheatmap pillar pkgconfig proxy purrr quadprog R6 ragg rappdirs RColorBrewer Rcpp rlang rmarkdown s2 S7 sass scales sf stringi stringr survival sys systemfonts textshaping tibble tidyr tidyselect timechange tinytex units utf8 uuid vctrs viridisLite withr wk xfun xml2 yaml yulab.utils zip zoo

Deconvolution of bulk RNA-seq data with granulator

Rendered fromgranulator.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Regress estimated cell type proportions against the ground truth	benchmark
PBMCs expression profiles (ABIS dataset)	bulkRNAseq_ABIS
Pearson correlation of cell type proportions across cell types and methods	correlate
Deconvolution from bulk RNAseq	deconvolute
Deconvolution methods acronyms	get_decon_methods
Convert raw counts to TPM	get_TPM
PBMCS true cell type proprotions (ABIS dataset)	groundTruth_ABIS
Load demo PBMCs deconvolution data	load_ABIS
Plot benchmarking analysis scores	plot_benchmark
Plot of correlations between deconvolution methods	plot_correlate
Estimated cell types across methods	plot_deconvolute
Plot estimated cell type proportions	plot_proportions
Plot estimated cell type coefficients against the ground truth	plot_regress
Plot reference profile similariy matrix	plot_similarity
Signature matrix for deconvolution of PBMCs in 17 cell types	sigMatrix_ABIS_S0
Signature matrix for deconvolution of PBMCs in 13 cell types	sigMatrix_ABIS_S1
Signature matrix for deconvolution of PBMCs in 11 cell types	sigMatrix_ABIS_S2
Signature matrix for deconvolution of PBMCs in 9 cell types	sigMatrix_ABIS_S3