CardinalIO
This is the released version of CardinalIO; for the devel version, see CardinalIO.
Read and write mass spectrometry imaging files
Bioconductor version: Release (3.23)
Fast and efficient reading and writing of mass spectrometry imaging data files. Supports imzML and Analyze 7.5 formats. Provides ontologies for mass spectrometry imaging.
Author: Kylie Ariel Bemis [aut, cre]
Maintainer: Kylie Ariel Bemis <k.bemis at northeastern.edu>
citation("CardinalIO")):
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("CardinalIO")
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("CardinalIO")| Parsing and writing imzML files | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, ImagingMassSpectrometry, Infrastructure, MassSpectrometry, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | Artistic-2.0 | file LICENSE |
| Depends | R (>= 4.4), BiocParallel, matter, ontologyIndex |
| Imports | methods, S4Vectors, stats, utils, tools |
| System Requirements | |
| URL | http://www.cardinalmsi.org |
| Bug Reports | https://github.com/kuwisdelu/CardinalIO/issues |
See More
| Suggests | BiocStyle, testthat, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | Cardinal |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CardinalIO_1.10.0.tar.gz |
| Windows Binary (x86_64) | CardinalIO_1.10.0.zip |
| macOS Binary (big-sur-x86_64) | CardinalIO_1.10.0.tgz |
| macOS Binary (sonoma-arm64) | CardinalIO_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CardinalIO |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CardinalIO |
| Bioc Package Browser | https://code.bioconductor.org/browse/CardinalIO/ |
| Package Short Url | https://bioconductor.org/packages/CardinalIO/ |
| Package Downloads Report | Download Stats |