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Spectre Home Page

Spectre is an R package and computational toolkit that enables comprehensive end-to-end integration, exploration, and analysis of high-dimensional cytometry, spatial/imaging, or single-cell data from different batches or experiments. Spectre streamlines the analytical stages of raw data pre-processing, batch alignment/integration, clustering, dimensionality reduction, visualisation, population annotation, and quantitative/statistical analysis; with a simple, clear, and modular design of analysis workflows, that can be utilised by both data and laboratory scientists. For more information see our about page and check our our metrics page for how Spectre has been used in the community. To get started, check out our getting started, protocols, or tutorial pages below.



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Getting started

Getting started with R, RStudio, and Spectre

Here we provide instructions for installing R, RStudio, and Spectre, along with introductory tutorials for getting started.


Protocols and tutorials

Cytometry (flow, mass, spectral)
Spatial and imaging
Single-cell genomics
Here we provide protocols and instructions for using Spectre for the integration and analysis of high-dimensional flow, spectral, or mass (CyTOF) cytometry data. Here we provide protocols and instructions for using Spectre for the spatial analysis of Imaging Mass Cytometry (IMC) data. Here we provide analysis options and tools to support scRNAseq analysis, in conjunction with existing tools such as Seurat and SingleCellExperiment.