Package: SPICEY
Title: Calculates cell type specificity from single cell data
Version: 1.2.0
Authors@R: c(
    person(given = "Georgina",
           family = "Fuentes-Páez",
           role = c("aut", "cre"),
           email = "georgina.fuentes@upf.edu",
           comment = c(ORCID = "0009-0003-9417-7148")),
    person(given = "Nacho",
           family = "Molina",
           role = c("aut"),
           email = "molinan@igbmc.fr"),
    person(given = "Mireia",
           family = "Ramos-Rodriguez",
           role = c("aut"),
           email = "mireia.ramos@upf.edu"),
    person(given = "Lorenzo",
           family = "Pasquali",
           role = c("aut"),
           email = "lorenzo.pasquali@upf.edu"), 
    person(given = "Ministerio de Ciencia e Innovación",
           family = "Spain",
           role = "fnd",
           comment = c("program" = "FPI Fellowship")))
Description: SPICEY (SPecificity Index for Coding and Epigenetic
        activitY) is an R package designed to quantify cell-type
        specificity in single-cell transcriptomic and epigenomic data,
        particularly scRNA-seq and scATAC-seq. It introduces two
        complementary indices: the Gene Expression Tissue Specificity
        Index (GETSI) and the Regulatory Element Tissue Specificity
        Index (RETSI), both based on entropy to provide continuous,
        interpretable measures of specificity. By integrating gene
        expression and chromatin accessibility, SPICEY enables
        standardized analysis of cell-type-specific regulatory programs
        across diverse tissues and conditions.
License: Artistic-2.0
Encoding: UTF-8
Depends: R (>= 4.5.0), utils, stats, grDevices
Imports: GenomicRanges, GenomicFeatures, AnnotationDbi, S4Vectors,
        ggplot2, dplyr, tidyr, tibble, GenomeInfoDb, scales, cowplot
Suggests: BiocStyle, knitr, rmarkdown,
        TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, testthat (>=
        3.0.0)
VignetteBuilder: knitr
biocViews: Transcriptomics, Epigenetics, SingleCell,
        DifferentialExpression, DifferentialPeakCalling,
        GeneRegulation, GeneTarget, GeneExpression, Transcription
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
URL: https://georginafp.github.io/SPICEY
BugReports: https://github.com/georginafp/SPICEY/issues
LazyData: false
Config/testthat/edition: 3
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 13:05:27 UTC
RemoteUrl: https://github.com/bioc/SPICEY
RemoteRef: RELEASE_3_23
RemoteSha: c3d422ae6d8e34ab62f1993c6ffbec18608604d4
NeedsCompilation: no
Packaged: 2026-10-10 15:21:09 UTC; root
Author: Georgina Fuentes-Páez [aut, cre] (ORCID:
    <https://orcid.org/0009-0003-9417-7148>),
  Nacho Molina [aut],
  Mireia Ramos-Rodriguez [aut],
  Lorenzo Pasquali [aut],
  Ministerio de Ciencia e Innovación Spain [fnd] (program: FPI
    Fellowship)
Maintainer: Georgina Fuentes-Páez <georgina.fuentes@upf.edu>