DOI: 10.18129/B9.bioc.quantiseqr  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see quantiseqr.

Quantification of the Tumor Immune contexture from RNA-seq data

Bioconductor version: 3.16

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>

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biocViews Annotation, Classification, ExperimentHubSoftware, FeatureExtraction, FlowCytometry, GeneExpression, ImmunoOncology, Microarray, Sequencing, Software, StatisticalMethod, Transcription, Transcriptomics, Visualization
Version 1.6.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License GPL-3
Depends R (>= 4.1.0)
Imports Biobase, limSolve, MASS, methods, preprocessCore, stats, SummarizedExperiment, ggplot2, tidyr, rlang, utils
Suggests AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat, tibble
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