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Interactive exploratory analysis with iSEE

Computational Biology Platform, Friedrich Miescher Institute for Biomedical Research

June 20, 2022

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Why (interactive) visualization?

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What is iSEE?

  • An open-source R/Bioconductor package that allows you to easily create customized interactive interfaces for exploring your data and visualize any pre-calculated results.

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What is iSEE?

  • An open-source R/Bioconductor package that allows you to easily create customized interactive interfaces for exploring your data and visualize any pre-calculated results.

  • Essentially data type agnostic - any rectangular data can be explored (but it was designed with high-throughput biological data in mind).

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What is iSEE?

  • An open-source R/Bioconductor package that allows you to easily create customized interactive interfaces for exploring your data and visualize any pre-calculated results.

  • Essentially data type agnostic - any rectangular data can be explored (but it was designed with high-throughput biological data in mind).

  • Easy to run (for a suitably formatted data set, more on that shortly):

    library(iSEE)
    iSEE(sce)
4 / 14

What is iSEE?

  • An open-source R/Bioconductor package that allows you to easily create customized interactive interfaces for exploring your data and visualize any pre-calculated results.

  • Essentially data type agnostic - any rectangular data can be explored (but it was designed with high-throughput biological data in mind).

  • Easy to run (for a suitably formatted data set, more on that shortly):

    library(iSEE)
    iSEE(sce)
  • Highly configurable, flexible interface.
4 / 14

What is iSEE?

  • An open-source R/Bioconductor package that allows you to easily create customized interactive interfaces for exploring your data and visualize any pre-calculated results.

  • Essentially data type agnostic - any rectangular data can be explored (but it was designed with high-throughput biological data in mind).

  • Easy to run (for a suitably formatted data set, more on that shortly):

    library(iSEE)
    iSEE(sce)
  • Highly configurable, flexible interface.

  • Strong focus on reproducibility, all code to generate displayed figures can be downloaded.

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Over 130 entries

With what data can iSEE be used?

  • Any form of (numeric) rectangular-shaped data (measurements for some form of features across a range of samples).
  • Both features and samples can come with annotations/additional information.
  • Data must be stored in a SummarizedExperiment container (or one of its derivatives, including SingleCellExperiment or DESeqDataSet).
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With what data can iSEE be used?

  • Any form of (numeric) rectangular-shaped data (measurements for some form of features across a range of samples).
  • Both features and samples can come with annotations/additional information.
  • Data must be stored in a SummarizedExperiment container (or one of its derivatives, including SingleCellExperiment or DESeqDataSet).
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How to get to a SummarizedExperiment/SingleCellExperiment object?

  • Use the constructor functions: SummarizedExperiment(), SingleCellExperiment(), DESeqDataSet(), DESeqDataSetFromMatrix(), ...

  • Many Bioconductor packages directly import data into a SingleCellExperiment object (e.g., DropletUtils::read10xCounts()) or a SummarizedExperiment object (e.g., tximeta::tximeta()).

  • From an AnnData object: use e.g. the zellkonverter Bioconductor package.

  • From a Seurat object: use e.g. Seurat::as.SingleCellExperiment().

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Default panels

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Some additional iSEEu panels (1)

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Some additional iSEEu panels (2)

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Some additional iSEEu panels (3)

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Some additional iSEEu panels (4)

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Additional resources



Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun
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Why (interactive) visualization?

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