Interactive design and validation of antibody panels using single-cell atlases | www.cytomarker.ai
Cytomarker enables iterative design of antibody panels using single-cell atlases. Key features:
- Pull scRNA-seq from Human Cell Atlas or upload custom data in common formats (
h5ad,Seurat,SingleCellExperiment) - Multiple visualizations and panel quality score to help design
- Identify marker redundancy and suggest substitutions
- Links to antibody databases to filter by application and find clone IDs
- The open-source version of Cytomarker hosted here contains antibody information parsed from the antibody registry
- The hosted version of Cytomarker contains proprietary antibody databases with additional information (e.g. antibody applications)
- To contribute additional antibody information, please contact us
For those with source code access to cytomarker, installation and access can be achieved through the following commands. Ensure that R and RStudio Desktop from Posit are installed for your specific operating system.
git clone https://github.com/camlab-bioml/cytomarker.git
cd cytomarker
Once cloned, open RStudio and import the project using File -> Open Project, and select the cytomarker.Rproj file. After importing the codebase, install the app dependencies:
library(devtools) # or, if devtools isn't installed
install.packages(c('devtools', 'remotes'))
This will prompt devtools to install all listed dependencies from the package.
Additional dependencies in R that are suggested by the package may also need to be explicitly installed:
additional_deps <- c('stringr',
'yardstick',
'htmltools',
'methods',
'stats',
'gridExtra',
'testthat',
'tools',
'scran',
'Seurat',
'caret',
'scuttle',
'scater',
'SummarizedExperiment',
'SingleCellExperiment',
'clustifyr',
'zellkonverter',
'printr',
'ggplot2',
'heatmaply',
'plotly')
BiocManager::install(additional_deps)
Once installed, the remaining dependencies should be automatically installed:
devtools::load_all();cytomarker()
In the command line, execute the following commands:
# navigate to the directory with the cytomarker source code
cd cytomarker
R -e 'devtools::load_all(); cytomarker()'
The final line will display a message providing the IP address and local port:
Listening on http://127.0.0.1:7665
Navigate to that IP address in your browser to run.
Alteratively, in the RStudio Desktop console:
devtools::load_all(); cytomarker()
- Matt Watson
- Eunice Poon
- Michael Geuenich
- Kieran Campbell