quantiseqr

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see quantiseqr.

Quantification of the Tumor Immune contexture from RNA-seq data


Bioconductor version: 3.17

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 "4.3") 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

Details

biocViews Annotation, Classification, ExperimentHubSoftware, FeatureExtraction, FlowCytometry, GeneExpression, ImmunoOncology, Microarray, Sequencing, Software, StatisticalMethod, Transcription, Transcriptomics, Visualization
Version 1.8.0
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
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.

Source Package quantiseqr_1.8.0.tar.gz
Windows Binary quantiseqr_1.8.0.zip
macOS Binary (x86_64) quantiseqr_1.8.0.tgz
macOS Binary (arm64) quantiseqr_1.8.0.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive