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# Cardinal ## Mass spectrometry imaging tools *Cardinal* provides an abstracted interface to manipulating mass spectrometry imaging datasets, simplifying most of the basic programmatic tasks encountered during the statistical analysis of imaging data. These include image manipulation and processing of both images and mass spectra, and dynamic plotting of both. While pre-processing steps including normalization, baseline correction, and peak-picking are provided, the core functionality of the package is statistical analysis. The package includes classification and clustering methods based on nearest shrunken centroids, as well as traditional tools like PCA and PLS. ## Installation ### Bioconductor Release *Cardinal* can be installed via the *BiocManager* package. ```{r install, eval=FALSE} if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Cardinal") ``` The same function can be used to update *Cardinal* and other Bioconductor packages. Once installed, *Cardinal* can be loaded with `library()`: ```{r library, eval=FALSE} library(Cardinal) ``` ### Bioconductor Devel The Bioconductor development version of *Cardinal* can also be installed via the *BiocManager* package. ```{r install, eval=FALSE} BiocManager::install("Cardinal", version="devel") ``` This version is unstable and should not be relied on for critical work. However, it is typically more stable than Github version. ### Github Devel The most cutting edge version of *Cardinal* can be installed from Github via the *remotes* package. ```{r install, eval=FALSE} if (!require("remotes", quietly = TRUE)) install.packages("remotes") remotes::github_install("kuwisdelu/Cardinal") ``` This version is unstable and only recommended for developers.