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scDiagnostics
This is thereleased version of scDiagnostics; for the devel version, seescDiagnostics.
Cell type annotation diagnostics
Bioconductor version: Release (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("scDiagnostics")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("scDiagnostics")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scDiagnostics")| 1. Getting Started with scDiagnostics | HTML | R Script |
| 2. Visualization of Cell Type Annotations | HTML | R Script |
| 3. Evaluation of Dataset and Marker Gene Alignment | HTML | R Script |
| 4. Detection and Analysis of Annotation Anomalies | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation,Classification,Clustering,GeneExpression,RNASeq,SingleCell,Software,Transcriptomics |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (1 year) |
| 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 |
| Bug Reports | https://github.com/ccb-hms/scDiagnostics/issues |
See More
| Suggests | AUCell,BiocStyle,knitr,rmarkdown,scran,scRNAseq,SingleR,celldex,scuttle,scater,dplyr,ComplexHeatmap, grid,testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | scDiagnostics_1.4.0.tar.gz |
| Windows Binary (x86_64) | scDiagnostics_1.4.0.zip |
| macOS Binary (x86_64) | scDiagnostics_1.4.0.tgz |
| macOS Binary (arm64) | scDiagnostics_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scDiagnostics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scDiagnostics |
| Bioc Package Browser | https://code.bioconductor.org/browse/scDiagnostics/ |
| Package Short Url | https://bioconductor.org/packages/scDiagnostics/ |
| Package Downloads Report | Download Stats |