iUSEiSEE

The iSEE package is a flexible, powerful and extendible application to explore any dataset stored in SummarizedExperiment objects, including single cell and spatially resolved data.

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

How to install 

library("remotes")
remotes::install_github("imbeimainz/iUSEiSEE", 
                        dependencies = TRUE, 
                        build_vignettes = TRUE)

How to run this workshop

  • Open the iUSEiSEE.Rproj project file
  • Navigate to the vignettes folder
  • Make sure the datasets are included in the datasets subfolder (if using Seurat or AnnData)
  • Open the individual Rmarkdown files and execute their content live!

Schedule

  • Short presentation, iSEE: Harry met Sally for interactive and reproducible data exploration
  • Installation of the dependencies & tech check
  • Retrieval of the data + Inspecting the processing steps so far
  • Overview on iSEE: panel by panel, learning Data + Visual + Selection parameters
  • Hands on with the full workshop
  • Going through the iSEE cookbook: “What if all I need is some recipes?”
  • Latest developments in the iSEE universe: iSEE for DE and pathways
  • Got more than just one dataset? iSEEhub and iSEEindex
  • iSEEfier: starting things up in a breeze
  • Got some own data? Some space for additional questions and setting up iSEE on that