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Cardinal

A mass spectrometry imaging toolbox for statistical analysis


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews Classification, Clustering, ImagingMassSpectrometry, ImmunoOncology, Infrastructure, Lipidomics, MassSpectrometry, Normalization, Proteomics, Regression, Software
Version 3.4.3
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 CardinalIO, Biobase, irlba, Matrix, matter, magrittr, mclust, nlme, parallel, signal, stats4, utils, viridisLite
System Requirements
URL http://www.cardinalmsi.org
See More
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_3.4.3.tar.gz
Windows Binary Cardinal_3.4.3.zip (64-bit only)
macOS Binary (x86_64) Cardinal_3.4.3.tgz
macOS Binary (arm64) Cardinal_3.4.3.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 3.18 Source Archive