DESCRIPTION

Package: quantiseqr
Title: Quantification of the Tumor Immune contexture from RNA-seq data
Version: 1.15.0
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