Cardinal

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Cardinal.

A mass spectrometry imaging toolbox for statistical analysis

Bioconductor version: 3.16

Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.

Author: Kylie A. Bemis <k.bemis at northeastern.edu>

Maintainer: Kylie A. Bemis <k.bemis at northeastern.edu>

Citation (from within R, enter citation("Cardinal")):

Installation

To install this package, start R (version "4.2") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("Cardinal")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Cardinal")

1. Cardinal 2: User guide for mass spectrometry imaging analysis HTML R Script

2. Cardinal 3: Statistical methods for mass spectrometry imaging HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, Clustering, ImagingMassSpectrometry, ImmunoOncology, Infrastructure, Lipidomics, MassSpectrometry, Normalization, Proteomics, Regression, Software

Version 3.0.1

In Bioconductor since BioC 3.1 (R-3.2) (9 years)

License Artistic-2.0

Depends ProtGenerics, BiocGenerics, BiocParallel, EBImage, graphics, methods, S4Vectors(>= 0.27.3), stats

Imports Biobase, irlba, Matrix, matter, magrittr, mclust, nlme, parallel, signal, sp, stats4, utils, viridisLite

System Requirements

URL http://www.cardinalmsi.org

Suggests BiocStyle, testthat, knitr, rmarkdown

Linking To

Enhances

Depends On Me CardinalWorkflows

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Cardinal_3.0.1.tar.gz

Windows Binary Cardinal_3.0.1.zip (64-bit only)

macOS Binary (x86_64) Cardinal_3.0.1.tgz

macOS Binary (arm64) Cardinal_3.0.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/Cardinal

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Cardinal

Bioc Package Browser https://code.bioconductor.org/browse/Cardinal/

Package Short Url https://bioconductor.org/packages/Cardinal/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.16 Source Archive