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Bioconductor - quantiseqr (development version)

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 (3.22)

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] ORCID: 0000-0003-3252-7758 , Francesca Finotello [aut] ORCID: 0000-0003-0712-4658

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

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

To install this package, start R (version "4.5") 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")
Details biocViews Annotation, Classification, ExperimentHubSoftware, FeatureExtraction, FlowCytometry, GeneExpression, ImmunoOncology, Microarray, Sequencing, Software, StatisticalMethod, Transcription, Transcriptomics, Visualization Version 1.17.0 In Bioconductor since BioC 3.13 (R-4.1) (4 years) License GPL-3 Depends R (>= 4.1.0) Imports Biobase, limSolve, MASS, methods, preprocessCore, stats, SummarizedExperiment, ggplot2, tidyr, rlang, utils System Requirements URL See More Suggests AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat, tibble Linking To Enhances Depends On Me Imports Me easier Suggests Me Links To Me Build Report Build Report Package Archives

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

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