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iUSEiSEE

The iSEE package is a flexible, powerful and extensible application to explore any dataset stored in a SummarizedExperiment object. In turn, any dataset that can be shaped into one or more numerical matrices (“rectangular” datasets) can easily be put into a SummarizedExperiment object. This includes many types of bulk, single cell and spatially resolved biological data, as well as many non-biological data types.

iSEE enables a multitude of panels to gain in-depth insight in your data; it does so combining interactivity and reproducibility, and provides an ideal tool for deeper dives into your data.

How to install

To follow this workshop, first install R and RStudio, e.g. following the instructions here. Next, within an R session, the workshop package and all required dependencies can be installed from GitHub as follows:

install.packages("BiocManager")
BiocManager::install("iSEE/iUSEiSEE",
                     dependencies = TRUE,
                     build_vignettes = TRUE)

How to run this workshop

  • Clone the GitHub repository to a local folder on your computer.
  • Open the iUSEiSEE.Rproj project file in RStudio.
  • Navigate to the vignettes folder.
  • Open the individual R Markdown files and execute their content live!

Schedule

  • Installation of the dependencies and tech check.
  • Retrieval and inspection of example data.
  • Overview of iSEE: panel by panel, learning Data + Visual + Selection parameters.
  • Hands-on practice using the recipes from the iSEE cookbook.
  • Exploring extension packages from the iSEE universe: iSEEde and iSEEpathways for differential expression and pathways, iSEEhub and iSEEindex for managing multiple datasets.
  • Easy generation of initial configurations with iSEEfier.
  • Definition of a new, custom panel type.

Need help?

If you encounter a problem while running iUSEiSEE, please open an issue and describe the problem. Make sure to provide a reproducible example, including your session info.

How to contribute

If you would like to contribute to iUSEiSEE, you can do so by sending a pull request to this repository. For large changes, we encourage you to first open an issue to discuss the intended contribution.

Code of conduct

Please note that the iSEE project (including iUSEiSEE) is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.