scDiagnostics
Diagnostic functions to assess the quality of cell type annotations in single-cell RNA-seq data
Science Score: 26.0%
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○Scientific vocabulary similarity
Low similarity (14.7%) to scientific vocabulary
Repository
Diagnostic functions to assess the quality of cell type annotations in single-cell RNA-seq data
Basic Info
- Host: GitHub
- Owner: ccb-hms
- Language: R
- Default Branch: main
- Homepage: https://ccb-hms.github.io/scDiagnostics/
- Size: 111 MB
Statistics
- Stars: 9
- Watchers: 6
- Forks: 2
- Open Issues: 6
- Releases: 0
Metadata Files
README.md
scDiagnostics: diagnostic functions to assess the quality of cell type annotations in single-cell RNA-seq data
Overview
The accurate annotation of cell types is a critical step in single-cell RNA-sequencing (scRNA-seq) analysis. While annotation transfer from a reference dataset offers a convenient and automated approach, it can also introduce biases and errors if not performed carefully.
scDiagnostics is an R package designed to address this challenge by providing a comprehensive set of diagnostic tools for evaluating the quality of cell type annotations in scRNA-seq data. With scDiagnostics, researchers can systematically assess the compatibility and accuracy of annotations, ensuring reliable and reproducible results in their scRNA-seq analysis workflow.
Installation
Installation from Bioconductor (Release)
Users interested in using the stable release version of the scDiagnostics package: please follow the installation instructions here. This is the recommended way of installing the package.
Installation from GitHub (Development)
To install the development version of the package from GitHub use the following command:
r
BiocManager::install("ccb-hms/scDiagnostics")
To build the package vignettes upon installation use:
r
BiocManager::install("ccb-hms/scDiagnostics",
build_vignettes = TRUE,
dependencies = TRUE)
Usage
See the scDiagnostics website for an overview of the functionality of the package. The individual documentation of each available function incl. usage details and executable examples is available in the reference tab.
Key Features
See the Getting Started with scDiagnostics vignette for an overview of the main functionality of the package. As listed below, additional vignettes are available for specific diagnostic tasks.
Visualization of Cell Type Annotations: Illustrates the distributions of cell type annotations of the query and reference dataset, allowing the user to identify potential differences in the cell type composition between datasets. Also provides functionality for assessing the impact of frequently used QC criteria on the cell type annotation confidence, allowing the user to identify systematic relationships between QC metrics and the predicted cell type categories.
Evaluation of Dataset and Marker Gene Alignment: Provides functionality for assessing dataset alignment through quantitative comparison of query-to-reference projections in reduced dimension space. Additional functionality for assessing marker gene expression across datasets allows the user to identify potential misalignments between reference and query on the level of individual genes.
Detection and Analysis of Annotation Anomalies: Focuses on identifying inconsistencies or anomalies in cell type annotations between the query and reference datasets through comparison of expert annotations with annotations derived from automated methods. By highlighting discrepancies that could be indicative of potential errors, this feature aids in refining and improving the accuracy and reliability of cell type classifications.
Owner
- Name: Center for Computational Biomedicine
- Login: ccb-hms
- Kind: organization
- Location: United States of America
- Website: https://computationalbiomed.hms.harvard.edu
- Repositories: 19
- Profile: https://github.com/ccb-hms
Harvard Medical School
GitHub Events
Total
- Issues event: 2
- Watch event: 7
- Issue comment event: 2
- Push event: 46
- Pull request event: 4
- Create event: 2
Last Year
- Issues event: 2
- Watch event: 7
- Issue comment event: 2
- Push event: 46
- Pull request event: 4
- Create event: 2
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 2
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- AnthonyChristidis (11)
- lgeistlinger (6)
- rgentlem (1)
- nturaga (1)
Pull Request Authors
- AnthonyChristidis (36)
- nturaga (4)
- andrewGhazi (3)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 2,230 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
bioconductor.org: scDiagnostics
Cell type annotation diagnostics
- Homepage: https://github.com/ccb-hms/scDiagnostics
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/scDiagnostics/inst/doc/scDiagnostics.pdf
- License: Artistic-2.0
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Latest release: 1.2.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- JamesIves/github-pages-deploy-action releases/v4 composite
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/upload-artifact master composite
- docker/build-push-action v4 composite
- docker/login-action v2 composite
- docker/setup-buildx-action v2 composite
- docker/setup-qemu-action v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- R >= 4.2.0 depends
- SingleCellExperiment * depends
- isotree * imports
- AUCell * suggests
- BiocStyle * suggests
- Matrix * suggests
- RColorBrewer * suggests
- SingleR * suggests
- SummarizedExperiment * suggests
- corrplot * suggests
- ggplot2 * suggests
- gridExtra * suggests
- knitr * suggests
- rmarkdown * suggests
- scRNAseq * suggests
- scater * suggests
- scran * suggests
- JamesIves/github-pages-deploy-action v4.5.0 composite
- actions/checkout v4 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite