quantiseqr

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see quantiseqr.

Quantification of the Tumor Immune contexture from RNA-seq data

Bioconductor version: 3.21

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 iD ORCID: 0000-0003-3252-7758 , Francesca Finotello [aut] ORCID iD 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")
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

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, Classification, ExperimentHubSoftware, FeatureExtraction, FlowCytometry, GeneExpression, ImmunoOncology, Microarray, Sequencing, Software, StatisticalMethod, Transcription, Transcriptomics, Visualization

Version 1.16.0

In Bioconductor since BioC 3.13 (R-4.1) (4.5 years)

License GPL-3

Depends R (>= 4.1.0)

Imports Biobase, limSolve, MASS, methods, preprocessCore, stats, SummarizedExperiment, ggplot2, tidyr, rlang, utils

System Requirements

URL

Suggests AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat, tibble

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

Source Package quantiseqr_1.16.0.tar.gz

Windows Binary (x86_64) quantiseqr_1.16.0.zip

macOS Binary (x86_64) quantiseqr_1.16.0.tgz

macOS Binary (arm64) quantiseqr_1.16.0.tgz

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/

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