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").
Version: 0.1.0 Imports: data.table, reshape2, dplyr, ggplot2, scales, pheatmap, cluster, factoextra, dendextend, Seurat, tidyselect, stringr, magrittr, tibble, futile.logger, mltools, utils Suggests: testthat (≥ 3.0.0), enrichR (≥ 3.0) Published: 2025-01-23 DOI: 10.32614/CRAN.package.SlideCNA Author: Diane Zhang [aut, cre], Johanna Klughammer [aut], Jan Watter [aut], Broad Institute of MIT and Harvard [cph, fnd] Maintainer: Diane Zhang <dkzhang711 at gmail.com> License: GPL (≥ 3) NeedsCompilation: no Materials: README NEWS CRAN checks: SlideCNA results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=SlideCNA to link to this page.
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