Package: CardinalIO 1.5.0

Kylie Ariel Bemis

CardinalIO: Read and write mass spectrometry imaging files

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.

Authors:Kylie Ariel Bemis [aut, cre]

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CardinalIO.pdf |CardinalIO.html✨
CardinalIO/json (API)
NEWS

# Install 'CardinalIO' in R:

install.packages('CardinalIO', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kuwisdelu/cardinalio/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:CardinalIO-1.5.0(bioc 3.21)CardinalIO-1.4.0(bioc 3.20)

software infrastructure dataimport massspectrometry imagingmassspectrometry cpp

5.41 score 1 stars 1 packages 3 scripts 278 downloads 12 exports 19 dependencies

Last updated 2 months agofrom:60442d0d0d. Checks:OK: 7 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win-x86_64	NOTE	Nov 29 2024
R-4.5-linux-x86_64	NOTE	Nov 29 2024
R-4.4-win-x86_64	OK	Nov 29 2024
R-4.4-mac-x86_64	OK	Nov 29 2024
R-4.4-mac-aarch64	OK	Nov 29 2024
R-4.3-win-x86_64	OK	Oct 15 2024
R-4.3-mac-x86_64	OK	Oct 15 2024
R-4.3-mac-aarch64	OK	Oct 15 2024

Exports:exampleImzMLFile find_descendants_in find_term find_terms get_obo ImzMeta metadata parseAnalyze parseImzML valid_terms writeAnalyze writeImzML

Dependencies:BH BiocGenerics BiocParallel codetools cpp11 digest formatR futile.logger futile.options generics irlba lambda.r lattice Matrix matter ontologyIndex ProtGenerics S4Vectors snow

CardinalIO: Parsing and writing imzML files

Kylie Ariel Bemis

Rendered fromCardinalIO-guide.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-08-12
Started: 2023-08-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
CardinalIO package	CardinalIO-package CardinalIO
Example imzML files	exampleImzMLFile
Mass spectrometry imaging ontology	find_descendants_in find_term find_terms get_obo valid_terms
Mass spectrometry imaging experimental metadata	class:ImzMeta ImzMeta ImzMeta-class [[<-,ImzMeta-method
Parse an Analyze 7.5 File	Analyze75 Analyze75-class class:Analyze75 parseAnalyze
Parse an imzML File	class:ImzML ImzML ImzML-class parseImzML
Write an Analyze 7.5 File	writeAnalyze writeAnalyze,array-method writeAnalyze,matter_arr-method writeAnalyze,sparse_arr-method
Write an imzML File	writeImzML writeImzML,ImzMeta-method writeImzML,ImzML-method