Package: SlideCNA
Title: Calls Copy Number Alterations from Slide-Seq Data
Version: 0.1.0
Authors@R: 
    c(person(given = "Diane",
           family = "Zhang",
           role = c("aut", "cre"),
           email = "dkzhang711@gmail.com",
           comment = c(ORCID = "0000-0002-0268-4413")),
      person(given = "Johanna",
           family = "Klughammer",
           role = c("aut"),
           email = "klughammer@genzentrum.lmu.de",
           comment = c(ORCID = "0000-0002-3628-9278")),
      person(given = "Jan",
           family = "Watter",
           role = c("aut"),
           email = "jan.watter@gmail.com",
           comment = c(ORCID = "0000-0001-7519-731X")),
      person("Broad Institute of MIT and Harvard", role = c("cph", "fnd")))
Description: This takes spatial single-cell-type RNA-seq data (specifically designed for Slide-seq v2) that calls copy number alterations (CNAs) using pseudo-spatial binning, clusters cellular units (e.g. beads) based on CNA profile, and visualizes spatial CNA patterns. Documentation about 'SlideCNA' is included in the the pre-print by Zhang et al. (2022, <doi:10.1101/2022.11.25.517982>). The package 'enrichR' (>= 3.0), conditionally used to annotate SlideCNA-determined clusters with gene ontology terms, can be installed at <https://github.com/wjawaid/enrichR> or with install_github("wjawaid/enrichR").
Imports: data.table, reshape2, dplyr, ggplot2, scales, pheatmap,
        cluster, factoextra, dendextend, Seurat, tidyselect, stringr,
        magrittr, tibble, futile.logger, mltools, utils
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.3.2
Suggests: testthat (>= 3.0.0), enrichR (>= 3.0)
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2025-01-22 04:05:22 UTC; dzhang
Author: Diane Zhang [aut, cre] (<https://orcid.org/0000-0002-0268-4413>),
  Johanna Klughammer [aut] (<https://orcid.org/0000-0002-3628-9278>),
  Jan Watter [aut] (<https://orcid.org/0000-0001-7519-731X>),
  Broad Institute of MIT and Harvard [cph, fnd]
Maintainer: Diane Zhang <dkzhang711@gmail.com>
Repository: CRAN
Date/Publication: 2025-01-23 17:40:05 UTC
Built: R 4.6.0; ; 2026-04-25 14:15:46 UTC; unix
