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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 |
Documentation:
Downloads:
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.