Package: signifinder
Type: Package
Title: Collection and implementation of public transcriptional cancer
        signatures
Version: 1.12.0
Authors@R: c(person("Stefania", "Pirrotta", role = c("cre", "aut"),
                    email = "stefania.pirrotta@phd.unipd.it",
                    comment = c(ORCID = "0009-0004-0030-217X")),
             person("Enrica", "Calura", role = "aut", 
                    email = "enrica.calura@unipd.it",
                    comment = c(ORCID = "0000-0001-8463-2432")))
Description: signifinder is an R package for computing and exploring a
        compendium of tumor signatures. It allows to compute a variety
        of signatures coming from public literature, based on gene
        expression values, and return single-sample (-cell/-spot)
        scores. Currently, signifinder collects more than 70 distinct
        signatures, relating to multiple tumors and multiple cancer
        processes.
License: AGPL-3
biocViews: GeneExpression, GeneTarget, ImmunoOncology,
        BiomedicalInformatics, RNASeq, Microarray, ReportWriting,
        Visualization, SingleCell, Spatial, GeneSignaling
Imports: AnnotationDbi, BiocGenerics, ComplexHeatmap, consensusOV,
        cowplot, DGEobj.utils, dplyr, ensembldb, ggplot2, ggridges,
        GSVA, IRanges, magrittr, matrixStats, maxstat, methods,
        openair, org.Hs.eg.db, patchwork, RColorBrewer,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene, SpatialExperiment, stats,
        scales, SummarizedExperiment, survival, survminer, viridis
Encoding: UTF-8
RoxygenNote: 7.3.2
Depends: R (>= 4.4.0)
LazyData: false
Suggests: BiocStyle, edgeR, grid, kableExtra, knitr, limma, testthat
        (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
BugReports: https://github.com/CaluraLab/signifinder/issues
URL: https://github.com/CaluraLab/signifinder
Config/pak/sysreqs: cmake make libmagick++-dev gsfonts libbz2-dev
        libicu-dev libjpeg-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev perl libx11-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:19:34 UTC
RemoteUrl: https://github.com/bioc/signifinder
RemoteRef: RELEASE_3_22
RemoteSha: 4cc4ec4b4c3e87720708d5d2f0f8ff7eaceb45fb
NeedsCompilation: no
Packaged: 2025-11-11 17:49:54 UTC; root
Author: Stefania Pirrotta [cre, aut] (ORCID:
    <https://orcid.org/0009-0004-0030-217X>),
  Enrica Calura [aut] (ORCID: <https://orcid.org/0000-0001-8463-2432>)
Maintainer: Stefania Pirrotta <stefania.pirrotta@phd.unipd.it>
Built: R 4.5.2; ; 2025-11-12 03:10:02 UTC; windows
