Package: quantiseqr
Title: Quantification of the Tumor Immune contexture from RNA-seq data
Version: 1.19.0
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: 7.3.2
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-12-01 16:45:50 UTC
RemoteUrl: https://github.com/bioc/quantiseqr
RemoteRef: HEAD
RemoteSha: 800b9ffd5db36ce7bf0295cb2207d9aa1c539ccc
NeedsCompilation: no
Packaged: 2026-03-02 08:05:59 UTC; root
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 4.6.0; ; 2026-03-02 08:08:14 UTC; windows
