quantiseqr

DOI: 10.18129/B9.bioc.quantiseqr    

Quantification of the Tumor Immune contexture from RNA-seq data

Bioconductor version: Release (3.15)

This package provides a streamlined workflow for the quanTIseq method, developed to perform the quantification of the Tumor Immune contexture from RNA-seq data. The quantification is performed against the TIL10 signature (dissecting the contributions of ten immune cell types), carefully crafted from a collection of human RNA-seq samples. The TIL10 signature has been extensively validated using simulated, flow cytometry, and immunohistochemistry data.

Author: Federico Marini [aut, cre] , Francesca Finotello [aut]

Maintainer: Federico Marini <marinif at uni-mainz.de>

Installation

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

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

BiocManager::install("quantiseqr")

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("quantiseqr")

 

HTML	R Script	Using quantiseqr
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Classification, ExperimentHubSoftware, FeatureExtraction, FlowCytometry, GeneExpression, ImmunoOncology, Microarray, Sequencing, Software, StatisticalMethod, Transcription, Transcriptomics, Visualization
Version	1.4.1
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 years)
License	GPL-3
Depends	R (>= 4.1.0)
Imports	Biobase, limSolve, MASS, methods, preprocessCore, stats, SummarizedExperiment, ggplot2, tidyr, rlang, utils
LinkingTo
Suggests	AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat, tibble
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	easier
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	quantiseqr_1.4.1.tar.gz
Windows Binary	quantiseqr_1.4.1.zip
macOS Binary (x86_64)	quantiseqr_1.4.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/quantiseqr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/quantiseqr
Package Short Url	https://bioconductor.org/packages/quantiseqr/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.15	Source Archive