This is the development version of scDiagnostics; for the stable release version, see scDiagnostics.
Cell type annotation diagnosticsBioconductor version: Development (3.22)
The scDiagnostics package provides diagnostic plots to assess the quality of cell type assignments from single cell gene expression profiles. The implemented functionality allows to assess the reliability of cell type annotations, investigate gene expression patterns, and explore relationships between different cell types in query and reference datasets allowing users to detect potential misalignments between reference and query datasets. The package also provides visualization capabilities for diagnostics purposes.
Author: Anthony Christidis [aut, cre] ORCID: 0000-0002-4565-6279 , Andrew Ghazi [aut], Smriti Chawla [aut], Nitesh Turaga [ctb], Ludwig Geistlinger [aut], Robert Gentleman [aut]
Maintainer: Anthony Christidis <anthony-alexander_christidis at hms.harvard.edu>
Citation (from within R, entercitation("scDiagnostics")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("scDiagnostics")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scDiagnostics")Follow Installation instructions to use this package in your R session.
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