granulator

Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data

Bioconductor version: 3.23 · Package version: 1.20.0

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.

DOI: 10.18129/B9.bioc.granulator

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("granulator")

Details

Maintainer	Sabina Pfister <sabina.pfister@novartis.com>
Author	Sabina Pfister [aut, cre], Vincent Kuettel [aut], Enrico Ferrero [aut]
License	GPL-3
URL	https://github.com/xanibas/granulator
Bug Reports	https://github.com/xanibas/granulator/issues
Status	Deprecated
Source branch	RELEASE_3_23
Build report	Bioconductor build system, r-universe
biocViews	DifferentialExpression, GeneExpression, RNASeq, Regression, SingleCell, Software, StatisticalMethod, Transcriptomics
Package Short Url	https://bioconductor.org/packages/granulator/

Citation

From within R, enter citation("granulator"):

Sabina Pfister, Vincent Kuettel, Enrico Ferrero. granulator: Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data. doi:10.18129/B9.bioc.granulator, R package version 1.20.0, https://bioconductor.org/packages/granulator.

Generated from the package metadata; it may differ from the package's own citation.

Documentation

Deconvolution of bulk RNA-seq data with granulator

Dependencies

Depends: R (>= 4.1)

Imports: cowplot, e1071, epiR, dplyr, dtangle, ggplot2, ggplotify, grDevices, limSolve, magrittr, MASS, nnls, parallel, pheatmap, purrr, rlang, stats, tibble, tidyr, utils

Suggests: BiocStyle, knitr, rmarkdown, testthat

Reverse dependencies

Suggests Me (1): deconvR