Streamlining Omics Data Visualization with iSEE and iSEEfier - Workshop

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

Overview

How to install

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

How to use this workshop

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

Description

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 of iSEE, as well as introducing iSEEfier, a Bioconductor package and iSEE extension, designed to simplify the setup of iSEE instances, making it easier to create customized visualization sessions. The participant will learn how to use iSEE and how to create tailored initial states with iSEEfier for diverse data exploration goals.

Pre-requisites

• Basic knowledge of R syntax
• Familiarity with bulk or single-cell sequencing data
• Familiarity with the SummarizedExperiment 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)

Participation

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

R / Bioconductor packages used

• iSEE
• iSEEfier

Time outline

Activity	Time
Introduction to iSEE	15m
Introduction to iSEEfier	15m
Questions	10m

Workshop goals and objectives

Through this workshop, you will…

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