SlideCNA: Calls Copy Number Alterations from Slide-Seq Data
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 |
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