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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 (3.19)

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 "4.4") and enter:


if (!require("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")
Using quantiseqr HTML R Script
Reference Manual PDF

Details

biocViews Annotation, Classification, ExperimentHubSoftware, FeatureExtraction, FlowCytometry, GeneExpression, ImmunoOncology, Microarray, Sequencing, Software, StatisticalMethod, Transcription, Transcriptomics, Visualization
Version 1.11.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends R (>= 4.1.0)
Imports Biobase, limSolve, MASS, methods, preprocessCore, stats, SummarizedExperiment, ggplot2, tidyr, rlang, utils
System Requirements
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Suggests AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat, tibble
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Package Archives

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

Source Package quantiseqr_1.11.0.tar.gz
Windows Binary quantiseqr_1.11.0.zip
macOS Binary (x86_64) quantiseqr_1.11.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/quantiseqr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/quantiseqr
Bioc Package Browser https://code.bioconductor.org/browse/quantiseqr/
Package Short Url https://bioconductor.org/packages/quantiseqr/
Package Downloads Report Download Stats