quantiseqr

This is the released version of quantiseqr; for the devel version, see quantiseqr.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13

Quantification of the Tumor Immune contexture from RNA-seq data

Bioconductor version: Release (3.23)

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")):

Federico Marini, Francesca Finotello. quantiseqr: Quantification of the Tumor Immune contexture from RNA-seq data. doi:10.18129/B9.bioc.quantiseqr, R package version 1.20.0, https://bioconductor.org/packages/quantiseqr.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	1.20.0
In Bioconductor since	BioC 3.13 (R-4.1) (5.5 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
Linking To
Enhances
Depends On Me
Imports Me	easier
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	quantiseqr_1.20.0.tar.gz
Windows Binary (x86_64)	quantiseqr_1.20.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	quantiseqr_1.20.0.tgz
macOS Binary (sonoma-arm64)	quantiseqr_1.20.0.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