Interactive And Collaborative Exploration Of Large-Scale Transcriptomics Data With 
NextGen Omics UK 2021
kevinrue KevinRUE67 kevin-rue-albrecht
Kevin Rue-Albrecht, University of Oxford
2021-11-08
iSEE
Winners of the 1st RStudio Shiny Contest
"Most technically impressive"
Team effort
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| Kevin | Charlotte | Federico | Aaron |
Bioconductor
Release 3.13 (April 2021)
- 2042 software packages
- 406 experiment data packages
- 965 annotation packages
- 29 workflows
SingleCellExperiment
SingleCellExperiment & iSEE
Parameter boxes
Transmitted selections
Code tracker
Panel settings
Preconfigured applications
Define the initial state
initial <- list( ReducedDimensionPlot( PanelWidth = 6L, Type = "TSNE", ColorByColumnData = "Cluster" ))Alternatively
Use the panel settings exported from a past session.
Configure the app and launch!
app <- iSEE(pbmc3k, initial = initial)shiny::runApp(app)Guided tours
Developing new panels
AggregatedDotPlot, DynamicMarkerTable, DynamicReducedDimensionPlot, ...
Custom landing pages
More
Not only single-cell transcriptomics, but any rectangular experimental data set, e.g.
bulk assays (e.g., RNA-seq, ChIP-seq)
microarray
flow cytometry
...
- Voice recognition, with
iSEE(..., voice = TRUE)
- Online book Extending iSEE
References
Amezquita, R. A., A. T. L. Lun, E. Becht, et al. (2020). "Orchestrating single-cell analysis with Bioconductor". In: Nat Methods 17.2, pp. 137-145. ISSN: 1548-7105 (Electronic) 1548-7091 (Linking). DOI: 10.1038/s41592-019-0654-x. URL: https://www.ncbi.nlm.nih.gov/pubmed/31792435.
Rue-Albrecht, K., F. Marini, C. Soneson, et al. (2018). "iSEE: Interactive SummarizedExperiment Explorer". In: F1000Res 7, p. 741. ISSN: 2046-1402 (Print) 2046-1402 (Linking). DOI: 10.12688/f1000research.14966.1. URL: https://www.ncbi.nlm.nih.gov/pubmed/30002819.
Contact
The #isee channel of the Bioconductor Slack workspace. Join here!
The iSEE GitHub organization at https://github.com/iSEE
This presentation on GitHub at