Introduction | Installation | Structure of imzML files | XML | Binary | Continuous | Processed | Additional notes | Parsing imzML files | Experimental metadata | File description | Scan settings | Software | Instrument configuration | Data processing | Spectrum metadata | Positions | m/z metadata | Intensity metadata | Mass spectra | Tracking experimental metadata | The ImzMeta class | Conversion between ImzML and ImzMeta | Minimum reporting guidelines | Writing imzML files | Writing a file from ImzML metadata | Writing a file from ImzMeta metadata | Session information
Package: CardinalIO 1.10.0
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:
CardinalIO_1.10.0.tar.gz
CardinalIO_1.10.0.zip(r-4.7)CardinalIO_1.10.0.zip(r-4.6)CardinalIO_1.10.0.zip(r-4.5)
CardinalIO_1.10.0.tgz(r-4.6-x86_64)CardinalIO_1.10.0.tgz(r-4.6-arm64)CardinalIO_1.10.0.tgz(r-4.5-x86_64)CardinalIO_1.10.0.tgz(r-4.5-arm64)
CardinalIO_1.10.0.tar.gz(r-4.7-arm64)CardinalIO_1.10.0.tar.gz(r-4.7-x86_64)CardinalIO_1.10.0.tar.gz(r-4.6-arm64)CardinalIO_1.10.0.tar.gz(r-4.6-x86_64)
CardinalIO_1.10.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CardinalIO/json (API)
| # Install 'CardinalIO' in R: |
| install.packages('CardinalIO', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kuwisdelu/cardinalio/issues
On BioConductor:CardinalIO-1.11.0(bioc 3.24)CardinalIO-1.10.0(bioc 3.23)
softwareinfrastructuredataimportmassspectrometryimagingmassspectrometrycpp
Last updated from:dfdfec47c0 (on RELEASE_3_23). Checks:12 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 170 | ||
| linux-devel-arm64 | NOTE | 218 | ||
| linux-devel-x86_64 | NOTE | 243 | ||
| source / vignettes | OK | 242 | ||
| linux-release-arm64 | NOTE | 214 | ||
| linux-release-x86_64 | NOTE | 296 | ||
| macos-release-arm64 | NOTE | 112 | ||
| macos-release-x86_64 | NOTE | 287 | ||
| macos-oldrel-arm64 | NOTE | 116 | ||
| macos-oldrel-x86_64 | NOTE | 244 | ||
| windows-devel | NOTE | 170 | ||
| windows-release | NOTE | 172 | ||
| windows-oldrel | NOTE | 142 | ||
| wasm-release | OK | 151 |
Exports:exampleImzMLFilefind_descendants_infind_termfind_termsget_oboImzMetametadataparseAnalyzeparseImzMLvalid_termswriteAnalyzewriteImzML
Dependencies:BHBiocGenericsBiocParallelcodetoolscpp11digestformatRfutile.loggerfutile.optionsgenericsirlbalambda.rlatticeMatrixmatterontologyIndexProtGenericsS4Vectorssnow
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 |
