Cardinal
This is the released version of Cardinal; for the devel version, see Cardinal.
A mass spectrometry imaging toolbox for statistical analysis
Bioconductor version: Release (3.23)
Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.
Author: Kylie Ariel Bemis [aut, cre]
Maintainer: Kylie Ariel Bemis <k.bemis at northeastern.edu>
citation("Cardinal")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 3: User guide for mass spectrometry imaging analysis | HTML | R Script |
| 2. Cardinal 3: Statistical methods for mass spectrometry imaging | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, Clustering, ImagingMassSpectrometry, ImmunoOncology, Infrastructure, Lipidomics, MassSpectrometry, Normalization, Proteomics, Regression, Software |
| Version | 3.14.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 years) |
| License | Artistic-2.0 | file LICENSE |
| Depends | R (>= 4.4), BiocParallel, BiocGenerics, ProtGenerics, S4Vectors, methods, stats, stats4 |
| Imports | CardinalIO, Biobase, graphics, grDevices, irlba, Matrix, matter(>= 2.7.10), nlme, parallel, utils |
| System Requirements | |
| URL | http://www.cardinalmsi.org |
| Bug Reports | https://github.com/kuwisdelu/Cardinal/issues |
See More
| Suggests | BiocStyle, testthat, knitr, rmarkdown, emmeans, lme4, lmerTest |
| 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_3.14.0.tar.gz |
| Windows Binary (x86_64) | Cardinal_3.14.0.zip |
| macOS Binary (big-sur-x86_64) | Cardinal_3.14.0.tgz |
| macOS Binary (sonoma-arm64) | Cardinal_3.14.0.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 |