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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").
Getting started
Browse package contents
Package details |
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| 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> |
| License | GPL (>= 3) |
| Version | 0.1.0 |
| Package repository | View on CRAN |
| Installation |
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