Here we provide protocols and instructions for using Spectre for the analysis of high-dimensional flow, spectral, or mass (CyTOF) cytometry data. To get started, you can check out our Spectre tutorial. To get started with using R/RStudio, check out our brief introductory R tutorial. You can see the list of versions available via Docker at this link. Install a 'container' version of Spectre using Docker, that contains a pre-built environment with all the required packages necessary to use Spectre. Install R, RStudio, and Spectre from Docker Please note: the original functions and workflows for spatial analysis from SpectreMAP have now been directly incorporated in Spectre v0.5.0 and above. If you are unfamiliar with using R or RStudio, first check out this 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. Installing and updating Spectre package from Github Once you have installed R and RStudio, you can check out this Download the latest version of R and R Studio by visiting the links below. We recommend interacting with Spectre and the R code via RStudio. Option 1 - Install Spectre with R and RStudio 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). To receive updates, you can join our mailing list here.
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