Package: quantiseqr
Title: Quantification of the Tumor Immune contexture from RNA-seq data
Version: 1.16.0
Authors@R: 
    c(
        person(
            given = "Federico", family = "Marini", role = c("aut", "cre"), 
            email = "marinif@uni-mainz.de", comment = c(ORCID = "0000-0003-3252-7758")
        ),
        person(
            given = "Francesca", family = "Finotello", role = "aut", 
            email = "francesca.finotello@i-med.ac.at", comment = c(ORCID = "0000-0003-0712-4658")
        )
    )
Description: 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.
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
biocViews: GeneExpression, Software, Transcription, Transcriptomics,
        Sequencing, Microarray, Visualization, Annotation,
        ImmunoOncology, FeatureExtraction, Classification,
        StatisticalMethod, ExperimentHubSoftware, FlowCytometry
VignetteBuilder: knitr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
git_url: https://git.bioconductor.org/packages/quantiseqr
git_branch: RELEASE_3_21
git_last_commit: b7e6a47
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-15 23:16:47 UTC; biocbuild
Author: Federico Marini [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3252-7758>),
  Francesca Finotello [aut] (ORCID:
    <https://orcid.org/0000-0003-0712-4658>)
Maintainer: Federico Marini <marinif@uni-mainz.de>
Built: R 4.5.0; ; 2025-04-16 06:21:21 UTC; unix
