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Getting started

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You can install Spectre directly using R and RStudio, or install a pre-built R environment containing Spectre using Docker (this is a good option if you have trouble installing Spectre directly with R/RStudio).

Option 1 - Install Spectre with R and RStudio

Install R and RStudio

Spectre is a software package in 'R'. We recommend interacting with Spectre and the R code via RStudio. Download the latest version of R and R Studio by visiting the links below.

Download R (CRAN) | Download RStudio

Once you have installed R and RStudio, you can check out this tutorial to get familiar with using it.

R & RStudio tutorial

Installing and updating Spectre package from Github

Once you have installed R and RStudio, the instructions for install and updating Spectre from Github (current default choice) is described below on this page. If you are unfamiliar with using R or RStudio, first check out this tutorial .

Install from Github

Please note: the original functions and workflows for spatial analysis from SpectreMAP have now been directly incorporated in Spectre v0.5.0 and above.

Option 2 - Install Spectre using Docker

Install R, RStudio, and Spectre from Docker

Install a 'container' version of Spectre using Docker, that contains a pre-built environment with all the required packages necessary to use Spectre.

Install from Docker

You can see the list of versions available via Docker at this link.

Please note: the original functions and workflows for spatial analysis from SpectreMAP have now been directly incorporated in Spectre v0.5.0 and above.

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.

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Spatial (IMC) analysis

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

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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.

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Other

Spectre tutorials

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

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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