granulator
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see granulator.
Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data
Bioconductor version: Release (3.23)
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.
Author: Sabina Pfister [aut, cre], Vincent Kuettel [aut], Enrico Ferrero [aut]
Maintainer: Sabina Pfister <sabina.pfister at novartis.com>
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.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("granulator")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("granulator")| Deconvolution of bulk RNA-seq data with granulator | HTML |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Regression, SingleCell, Software, StatisticalMethod, Transcriptomics |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5.5 years) |
| License | GPL-3 |
| 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 |
| System Requirements | |
| URL | https://github.com/xanibas/granulator |
| Bug Reports | https://github.com/xanibas/granulator/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | deconvR |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/granulator |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/granulator |
| Package Short Url | https://bioconductor.org/packages/granulator/ |
| Package Downloads Report | Download Stats |