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
git_url: https://git.bioconductor.org/packages/SPICEY
git_branch: RELEASE_3_23
git_last_commit: c3d422a
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: no
Packaged: 2026-04-28 23:38:00 UTC; biocbuild
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>
Built: R 4.6.0; ; 2026-04-29 05:02:22 UTC; unix
