scDiagnostics
This is the development version of scDiagnostics; for the stable release version, see scDiagnostics.
Cell type annotation diagnostics
Bioconductor version: Development (3.24)
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] 
, 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("scDiagnostics")):Anthony Christidis, Andrew Ghazi, Smriti Chawla, Ludwig Geistlinger, Robert Gentleman. scDiagnostics: Cell type annotation diagnostics. doi:10.18129/B9.bioc.scDiagnostics, R package version 1.7.15, https://bioconductor.org/packages/scDiagnostics.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("scDiagnostics")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scDiagnostics")| 3. Case Study: A Disease-Associated Monocyte State in COVID-19 | HTML | R Script |
| 1. Introduction to scDiagnostics | HTML | R Script |
| 4. Case Study: An Inflamed Fibroblast State in Spatial Colitis Data | HTML | R Script |
| 2. Benchmarking Anomaly Detection Against Ground Truth | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Classification, Clustering, GeneExpression, RNASeq, SingleCell, Software, Transcriptomics |
| Version | 1.7.15 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0) |
| Imports | SingleCellExperiment, methods, isotree, FNN, igraph, ggplot2, GGally, ggridges, SummarizedExperiment, ranger, transport, cramer, rlang, bluster, scales, MASS, stringr, Matrix, grDevices |
| System Requirements | |
| URL | https://github.com/ccb-hms/scDiagnostics https://ccb-hms.github.io/scDiagnostics |
| Bug Reports | https://github.com/ccb-hms/scDiagnostics/issues |
See More
| Suggests | AUCell, BiocStyle, knitr, rmarkdown, scran, scRNAseq, SingleR, celldex, scuttle, scater, BiocSingular, dplyr, ComplexHeatmap, circlize, grid, ragg, splatter, SpatialExperiment, BiocFileCache, pROC, PRROC, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scDiagnostics_1.7.15.tar.gz |
| Windows Binary (x86_64) | scDiagnostics_1.7.15.zip |
| macOS Binary (big-sur-x86_64) | scDiagnostics_1.7.15.tgz |
| macOS Binary (sonoma-arm64) | scDiagnostics_1.7.15.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scDiagnostics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scDiagnostics |
| Package Short Url | https://bioconductor.org/packages/scDiagnostics/ |
| Package Downloads Report | Download Stats |