Package: PIUMA
Type: Package
Title: Phenotypes Identification Using Mapper from topological data
        Analysis
Version: 1.6.1
Authors@R: c(
    person("Mattia", "Chiesa", , "mattia.chiesa@cardiologicomonzino.it", 
	role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7427-9954")),
    person("Arianna", "Dagliati", , "arianna.dagliati@unipv.it",
	role = "aut", comment = c(ORCID = "0000-0002-5041-0409")),
	person("Alessia", "Gerbasi", , "alessia.gerbasi01@universitadipavia.it",
	role = "aut", comment = c(ORCID = "0000-0003-4501-1777")),
	person("Giuseppe", "Albi", , "giuseppe.albi01@universitadipavia.it",
	role = "aut"),
	person("Laura", "Ballarini", , "laura.ballarini01@universitadipavia.it",
	role = "aut"),
	person("Luca", "Piacentini", , "luca.piacentini@cardiologicomonzino.it",
	role = "aut", comment = c(ORCID = "0000-0003-1022-4481")),
	person("Carlo", "Leonardi", , "cl35@sanger.ac.uk",
    role = "aut",
           comment = c(ORCID = "0000-0001-5348-8300"))
  )
Description: The PIUMA package offers a tidy pipeline of Topological
        Data Analysis frameworks to identify and characterize
        communities in high and heterogeneous dimensional data.
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: false
biocViews: Clustering, GraphAndNetwork, DimensionReduction, Network,
        Classification
VignetteBuilder: knitr
Imports: Hmisc, igraph, patchwork, scales, utils, cluster, umap, tsne,
        kernlab, vegan, dbscan, grDevices, stats, methods,
        SummarizedExperiment, ggplot2
Suggests: BiocStyle, testthat, knitr, rmarkdown, Seurat,
        SingleCellExperiment, aricode, mclust, viridis, magick,
        ggrepel, dplyr
Depends: R (>= 4.3)
RoxygenNote: 7.3.1
URL: https://github.com/BioinfoMonzino/PIUMA
BugReports: https://github.com/BioinfoMonzino/PIUMA/issues
Config/pak/sysreqs: libglpk-dev make libicu-dev libpng-dev libxml2-dev
        libssl-dev python3 zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-02-04 07:43:31 UTC
RemoteUrl: https://github.com/bioc/PIUMA
RemoteRef: RELEASE_3_22
RemoteSha: 3ee55cdedf70cd03be491236b8bf50e65f14566c
NeedsCompilation: no
Packaged: 2026-03-07 04:06:32 UTC; root
Author: Mattia Chiesa [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7427-9954>),
  Arianna Dagliati [aut] (ORCID: <https://orcid.org/0000-0002-5041-0409>),
  Alessia Gerbasi [aut] (ORCID: <https://orcid.org/0000-0003-4501-1777>),
  Giuseppe Albi [aut],
  Laura Ballarini [aut],
  Luca Piacentini [aut] (ORCID: <https://orcid.org/0000-0003-1022-4481>),
  Carlo Leonardi [aut] (ORCID: <https://orcid.org/0000-0001-5348-8300>)
Maintainer: Mattia Chiesa <mattia.chiesa@cardiologicomonzino.it>
Built: R 4.5.2; ; 2026-03-07 04:08:36 UTC; windows
