Spectre Home About Citation Get started Protocols Tutorials Spatial Report Issue Q&A Github

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.



See our latest version

AppVeyor build status

To receive updates, you can join our mailing list here.

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.



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.

Citation: if you use Spectre in your work, please consider citing Ashhurst TM, Marsh-Wakefield F, Putri GH et al. (2021). Cytometry A. DOI: 10.1002/cyto.a.24350. To continue providing open-source tools such as Spectre, it helps us if we can demonstrate that our efforts are contributing to analysis efforts in the community. Please also consider citing the authors of the individual packages or tools (e.g. CytoNorm, FlowSOM, tSNE, UMAP, etc) that are critical elements of your analysis work. We have provided some generic text that you can use for your methods section with each protocol and on the ‘citation’ page.


Spectre tutorials

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