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Some materials in this workshop were adapted from resources created by theiSEE core development team (Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun)

library("remotes")remotes::install_github("NajlaAbassi/iSEEfierWorkshopSCBS2024",dependencies=TRUE,build_vignettes=TRUE)

• Install the package (with command above)
• Download this repo (https://github.com/NajlaAbassi/iSEEfierWorkshopSCBS2024)
• Unpack the downloaded folder
• Navigate to thevignettes folder
• Open theworkshop_iSEEfier.Rmd Rmarkdown file and execute its content live!

Effectively exploring and visualizing omics data is one crucial step for uncovering new biological insights.iSEE, a Bioconductor package/Shiny App, offers a wealth of powerful features to help you visualize your data at any stage of the data analysis pipeline.

This workshop will cover some of the core functionalities ofiSEE, as well as introducingiSEEfier, a Bioconductor package andiSEE extension, designed to simplify the setup ofiSEE instances, making it easier to create customized visualization sessions. The participant will learn how to useiSEE and how to create tailored initial states withiSEEfier for diverse data exploration goals.

• Basic knowledge of R syntax
• Familiarity with bulk or single-cell sequencing data
• Familiarity with theSummarizedExperiment class

Relevant background reading:

• Rue-Albrecht K, Marini F, Soneson C and Lun ATL. iSEE: Interactive SummarizedExperiment Explorer [version 1; peer review: 3 approved]. F1000Research 2018, 7:741 (https://doi.org/10.12688/f1000research.14966.1)
• iUSEiSEE workshop:materials
• Huber, W., Carey, V., Gentleman, R. et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods 12, 115–121 (2015). (https://doi.org/10.1038/nmeth.3252)

You are encouraged to ask questions throughout the workshop. You can also write questions during, and after the workshop using theNew issue button on the GitHub repository for this workshop.

• iSEE
• iSEEfier

Through this workshop, you will...

• see how easy it is to runiSEE.
• obtain a quick overview of the available panels and the user interface.
• learn how to seamlessly customize the initial configuration ofiSEE withiSEEfier for different visualization goals.