Package: granulator 1.13.0

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/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

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 BioConductor:granulator-1.13.0(bioc 3.20)granulator-1.12.0(bioc 3.19)

bioconductor-package

12 exports 0.49 score 116 dependencies

Last updated 2 months agofrom:e912228f91

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 colorspace commonmark cowplot cpp11 crayon crul curl data.table DBI DEoptimR digest dplyr dtangle e1071 epiR evaluate fansi farver fastmap flextable fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics gfonts ggplot2 ggplotify glue gridGraphics gtable highr htmltools httpcode httpuv isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lifecycle limSolve lpSolve lubridate magrittr MASS Matrix memoise mgcv mime munsell nlme nnls officer openssl pander pheatmap pillar pkgconfig promises proxy purrr quadprog R6 ragg rappdirs RColorBrewer Rcpp rlang rmarkdown s2 sass scales sf shiny sourcetools stringi stringr survival sys systemfonts textshaping tibble tidyr tidyselect timechange tinytex triebeard units urltools utf8 uuid vctrs viridisLite withr wk xfun xml2 xtable yaml yulab.utils zip zoo

Deconvolution of bulk RNA-seq data with granulator

Vincent Kuettel, Sabina Pfister, Enrico Ferrero

Rendered fromgranulator.Rmdusingknitr::rmarkdownon Jun 15 2024.

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