granulator

DOI: 10.18129/B9.bioc.granulator  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	DifferentialExpression, GeneExpression, RNASeq, Regression, SingleCell, Software, StatisticalMethod, Transcriptomics
Version	1.6.0
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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/xanibas/granulator
BugReports	https://github.com/xanibas/granulator/issues
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_1.6.0.tar.gz
Windows Binary	granulator_1.6.0.zip
macOS Binary (x86_64)	granulator_1.6.0.tgz
macOS Binary (arm64)	granulator_1.6.0.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