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SlideCNA  

Calls Copy Number Alterations from Slide-Seq Data
View on CRAN: Click here


Download and install SlideCNA package within the R console
Install from CRAN:
install.packages("SlideCNA")

Install from Github:
library("remotes")
install_github("cran/SlideCNA")

Install by package version:
library("remotes")
install_version("SlideCNA", "0.1.0")



Attach the package and use:
library("SlideCNA")
Maintained by
Diane Zhang
[Scholar Profile | Author Map]
First Published: 2025-01-23
Latest Update: 2025-01-23
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").
How to cite:
Diane Zhang (2025). SlideCNA: Calls Copy Number Alterations from Slide-Seq Data. R package version 0.1.0, https://cran.r-project.org/web/packages/SlideCNA. Accessed 03 May. 2025.
Previous versions and publish date:
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Complete documentation for SlideCNA
Functions, R codes and Examples using the SlideCNA R package
Full SlideCNA package functions and examples
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