BDI R Code Clinic – 1 July 11am, Microsoft Teams (link will be distributed week commencing 29 June)

Intuitive interactive data exploration with iSEE – Kevin Rue Albrecht

Please sign up here: oxford.onlinesurveys.ac.uk/bdi-r-code-clinic-1-july

Description

Exploratory analysis and visualization are integral parts of the analysis and communication of biological data, but are typically performed using static plots.

This tutorial will demonstrate how to use the iSEE R package ( bioconductor.org/packages/iSEE ) to instead create and customize interactive applications for the exploration of various types of biological data sets (e.g., bulk and single-cell RNA-seq, CyTOF, gene expression microarray), while maintaining reproducibility.

A running example of an app created with iSEE, including a tour guiding the user through the interface, is deployed at shiny.imbei.uni-mainz.de:3838/iSEE .

The tutorial will be presented as a brief introduction to key Bioconductor data structures followed by a demonstration of interactive visualisation following a standard single-cell RNA-sequencing workflow., guided by completely worked examples and stand-alone notes that participants may continue to use after the workshop.

Packages
iSEEWorkshop2020, github.com/iSEE/iSEEWorkshop2020https://github.com/iSEE/iSEEWorkshop2020
iSEE, bioconductor.org/packages/iSEE
iSEEu, bioconductor.org/packages/iSEEu
TENxPBMCData, bioconductor.org/packages/TENxPBMCData
scater, bioconductor.org/packages/scater
BiocSingular, bioconductor.org/packages/BiocSingular
scran, bioconductor.org/packages/scran
Rtsne, bioconductor.org/packages/Rtsne
uwot, bioconductor.org/packages/uwot
igraph, bioconductor.org/packages/igraph
Slides: isee.github.io/iSEEWorkshop2020Slides