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Exploring existing analyses

Before contributing to OpenScPCA, you can explore and run any existing analysis modules on your local machine.

You can browse existing analysis modules in the repository in the analyses folder. This folder also contains a pair of example analyses, one for performing analysis in R and one for performing analysis in Python.

To run the example analysis modules or any other existing modules, you will need to:

Set up your local environment

Before you can run any analysis modules locally, you need to set up your environment.

Please refer to these linked instructions for the specific setup steps you need to take.

Follow instructions to run existing modules

Each existing module has its own folder in the repository's analyses folder. See our documentation on analysis modules to learn more about how analyses are structured.

All instructions and files (except data) needed to run a given module are provided in the module's folder.

  • To run existing modules, please refer to the README.md found in the root directory of that module.
  • The README.md will contain a description of the module, instructions to run the module, the list of input and output files, and any additional software or computing resources you may need.

Get access to data for running modules

For modules that use data obtained from the ScPCA Portal as input, you can directly download data from the ScPCA Portal.

Additionally, you can use the simulate-sce analysis module to create simulated data:

  • This module simulates data based on the properties of real ScPCA data.
  • The simulated data contains permuted labels and simulated counts data for a small number of cells, making it ideal for testing analyses modules.
  • The module requires either SingleCellExperiment or AnnData objects from the ScPCA Portal as input.

In some cases, an analysis module's input data will be the results/output from a different module. These results are stored in an S3 bucket on Amazon Web Services, and are available to contributors. Read more about getting access to data.