Cytomarker

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

Get started

🖥️ Launch Cytomarker

📖 Read documentation

Supported antibody databases

• 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

Installation from source

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()

Running locally

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()

Developers

• Matt Watson
• Eunice Poon
• Michael Geuenich
• Kieran Campbell