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Getting started

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Installing Spectre

Installing and updating Spectre

Here we provide instructions for installing Spectre. Options include installing in R/RStudio or via Docker. If you are unfamiliar with using R or RStudio, first check out this tutorial .

Install Spectre

Introductory tutorials

R & RStudio tutorial

To get started with using R/RStudio, check out our brief introductory R tutorial.

R tutorial

Spectre tutorial

To get started, you can check out our Spectre tutorial.

Spectre tutorial

Analysis workflows and protocols

Spectre protocols for cytometry analysis

Here we provide protocols and instructions for using Spectre for the analysis of high-dimensional flow, spectral, or mass (CyTOF) cytometry data. This includes workflows and strategies for performing alignment/integration of data generated in different batches or experiments.


Spatial (IMC) analysis

Here we provide protocols and instructions for using Spectre for the spatial analysis of Imaging Mass Cytometry (IMC) data.


Support for scRNAseq analysis

Here we provide analysis options and tools to support scRNAseq analysis, in conjunction with existing tools such as Seurat and SingleCellExperiment.



Spectre tutorials

Here we provide tutorials and other worked examples for further education on Spectre and computational analysis more broadly.


Install a development version of Spectre

If you are interested in testing new features, or contributing your own, you can also install the development version of Spectre from Github. We suggested using in conjunction with our developers guide.

Install development version