quantiseqr

DOI: 10.18129/B9.bioc.quantiseqr    

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

Quantification of the Tumor Immune contexture from RNA-seq data

Bioconductor version: Development (3.14)

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>

Citation (from within R, enter citation("quantiseqr")):

Installation

To install this package, start R (version "4.1") and enter:

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

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

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 1.1.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package quantiseqr_1.1.0.tar.gz
Windows Binary quantiseqr_1.1.0.zip
macOS 10.13 (High Sierra) quantiseqr_1.1.0.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

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