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granulator

This is the development version of granulator; for the stable release version, see granulator.

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

Bioconductor version: Development (3.18)

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Deconvoluting bulk RNA-seq data with granulator HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, RNASeq, Regression, SingleCell, Software, StatisticalMethod, Transcriptomics
Version 1.9.0
In Bioconductor since BioC 3.13 (R-4.1) (2 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
Linking To
Suggests BiocStyle, knitr, rmarkdown, testthat
System Requirements
Enhances
URL https://github.com/xanibas/granulator
Bug Reports https://github.com/xanibas/granulator/issues
See More
Depends On Me
Imports Me
Suggests Me deconvR
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package granulator_1.9.0.tar.gz
Windows Binary granulator_1.9.0.zip
macOS Binary (x86_64) granulator_1.9.0.tgz
macOS Binary (arm64) granulator_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/granulator
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/granulator
Bioc Package Browser https://code.bioconductor.org/browse/granulator/
Package Short Url https://bioconductor.org/packages/granulator/
Package Downloads Report Download Stats