Page contents:
Installing R/RStudio (& XQuartz)
To get started, you will first need to download R, RStudio, and XQuartz (mac users only).
.
| Install R and RStudio (& XQuartz for mac users) | |||||||||||||||||||||
| Download the latest version of R by visiting https://cran.r-project.org/mirrors.html and selecting a mirror to download R. Download the latest version of R Studio by visiting https://rstudio.com/ and go to download.
| ||||||||||||||||||||
To get started with using R/RStudio, check out our brief introductory R tutorial:
| |||||||||||||||||||||
| For mac users only, X11 (including tcltk) requires XQuartz to be installed since it is no longer part of OS X. Always re-install XQuartz when upgrading your macOS to a new major version.
| ||||||||||||||||||||
Installing Spectre
Spectre is a package provided for use in R/RStudio. By default, you can download Spectre from our Github page. This page will be updated once our default installation location changes to CRAN or Bioconductor.
.
| DEFAULT: install from Github | ||||||||||||
| Instructions for install and updating Spectre from Github (current default choice) is described below on this page.
| |||||||||||
To get started, you can also check out our 'about Spectre' page and Spectre tutorial:
| ||||||||||||
If you intend to perform spatial analysis of Imaging Mass Cytometry (IMC) data, your will also need to install SpectreMAP.
| ||||||||||||
.
| Alternative installations | |||||||||||
| Install 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 a development version of Spectre (including the 'spatial analysis' branch) 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.
| ||||||||||
