Package: CAMERA 1.63.0

Steffen Neumann

CAMERA: Collection of annotation related methods for mass spectrometry data

Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments

Authors:Carsten Kuhl, Ralf Tautenhahn, Hendrik Treutler, Steffen Neumann {ckuhl|htreutle|sneumann}@ipb-halle.de, [email protected]

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CAMERA.pdf |CAMERA.html✨
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NEWS

# Install 'CAMERA' in R:
install.packages('CAMERA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/sneumann/camera/issues

Datasets:
  • mm14 - Extract of marker mixture 14 LC/MS data

On BioConductor:CAMERA-1.63.0(bioc 3.21)CAMERA-1.62.0(bioc 3.20)

immunooncologymassspectrometrymetabolomics

10.37 score 11 stars 6 packages 165 scripts 820 downloads 429 mentions 40 exports 150 dependencies

Last updated 2 months agofrom:1d980b7ec5. Checks:OK: 1 WARNING: 4 NOTE: 2 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-win-x86_64WARNINGNov 30 2024
R-4.5-linux-x86_64WARNINGNov 30 2024
R-4.4-win-x86_64WARNINGNov 30 2024
R-4.4-mac-x86_64ERRORNov 30 2024
R-4.4-mac-aarch64WARNINGNov 30 2024
R-4.3-win-x86_64NOTENov 30 2024
R-4.3-mac-x86_64ERRORNov 30 2024
R-4.3-mac-aarch64NOTENov 30 2024

Exports:annotateannotateDiffreportcalcCaScalcCiScalcIsotopescalcPCcalcPC.hcscalcPC.lpccleanParallelcombinexsAnnoscompoundLibrariescompoundQuantilesfindAdductsfindIsotopesfindIsotopesWithValidationfindKendrickMassesfindNeutralLossfindNeutralLossSpecsgenerateRulesgetAllPeakEICsgetAtomCountgetIsotopeClustergetIsotopeProportiongetPeaklistgetpspectragetReducedPeaklistgroupCorrgroupDengroupFWHMmassWindowSizesplotEICsplotPsSpectrumpspec2metfragpspec2metfusionreadListssetDefaultListssetDefaultParamssetParamsshowxsAnnotate

Dependencies:abindaffyaffyioAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbslibcachemcheckmatecliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmennetopensslpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchpurrrQFeaturesR6rappdirsRBGLRColorBrewerRcppreshape2Rhdf5librlangrmarkdownrpartrstudioapiS4ArraysS4VectorssassscalessnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisviridisLitevsnwithrxcmsxfunXMLXVectoryamlzlibbioc

Atom count expectations with compoundQuantiles

Rendered fromcompoundQuantilesVignette.Rnwusingutils::Sweaveon Nov 30 2024.

Last update: 2019-12-02
Started: 2016-09-23

Isotope pattern validation with CAMERA

Rendered fromIsotopeDetectionVignette.Rnwusingutils::Sweaveon Nov 30 2024.

Last update: 2022-02-08
Started: 2016-09-28

Molecule Identification with CAMERA

Rendered fromCAMERA.Rnwusingutils::Sweaveon Nov 30 2024.

Last update: 2022-02-08
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Automatic deconvolution/annotation of LC/ESI-MS dataannotate annotate,xcmsSet-method
Automatic deconvolution/annotation of LC/ESI-MS dataannotateDiffreport annotateDiffreport,xsAnnotate-methods
EIC correlation grouping of LC/ESI-MS datacalcCaS calcCaS,xsAnnotate-method
Calculate peak distance matrix after EIC correlationcalcCiS calcCiS,xsAnnotate-method
Calculate isotope distance matrix from xsAnnotate objectcalcIsotopes calcIsotopes,xsAnnotate-method
Peakclustering into pseudospectra according to a distance matrixcalcPC calcPC,calcPC-method calcPC,xsAnnotate-method
Peakclustering into pseudospectra with the highly connected subgraphs approachcalcPC.hcs calcPC.hcs,xsAnnotate-method
Peakclustering into pseudospectra with the label-propagation-community algorithmcalcPC.lpc calcPC.lpc,xsAnnotate-method
Cleans up with spawned slave processes after usecleanParallel
Check CAMERA ion species annotation due to matching with opposite ion modecombinexsAnnos
The supported compound databasescompoundLibraries
compoundQuantiles constructorcompoundQuantiles
Class compoundQuantiles encapsulates compound statistics from different databases.compoundQuantiles-class
Calculate Adducts and Annotate LC/ESI-MS SpectrafindAdducts findAdducts,xsAnnotate-method
Deconvolute/Annotate LC/ESI-MS datafindIsotopes findIsotopes,xsAnnotate-method
Deconvolute/Annotate LC/ESI-MS datafindIsotopesWithValidation findIsotopesWithValidation,xsAnnotate-method
Find specfic mass defects using Kendrick mass scalesfindKendrickMasses
Find pseudospectra that contains a specific neutral lossfindNeutralLoss
Find pseudospectra that contains a specific neutral lossfindNeutralLossSpecs
Generate EIC information from raw datagetAllPeakEICs getAllPeakEICs,xsAnnotate-method
The number of atoms of the given elementgetAtomCount getAtomCount,compoundQuantiles-method
Retrieve the annotatad isotopesgetIsotopeCluster
The proportion of the intensities of two isotope peaksgetIsotopeProportion getIsotopeProportion,compoundQuantiles-method
Generate the annotatad peaklistgetPeaklist getPeaklist,xsAnnotate-method
Retrieve a peaklist of one or more pseudospectragetpspectra
Generate reduced peaklist from the annotatad peaklistgetReducedPeaklist getReducedPeaklist,xsAnnotate-method
EIC correlation grouping of LC/ESI-MS datagroupCorr groupCorr,xsAnnotate-method
Density-Grouping of LC/ESI-MS datagroupDen groupDen,xsAnnotate-method
FWHM-Grouping of LC/ESI-MS datagroupFWHM groupFWHM,xsAnnotate-method
The supported mass window sizesmassWindowSizes
Extract of marker mixture 14 LC/MS datamm14
Plot extracted ion chromatograms from (multiple) PseudospectraplotEICs plotEICs,xsAnnotate-method plotEICs.xsAnnotate
Plot a PseudospectrumplotPsSpectrum plotPsSpectrum,xsAnnotate-method plotPsSpectrum.xsAnnotate
Distance methods for xsAnnotatepsDist psDist,CAMERA-method psDist-methods
Export the putative fragments as MetFrag query filespspec2metfrag pspec2metfusion
Class 'ruleSet'class:ruleSet generateRules generateRules,ruleSet-method readLists readLists,ruleSet-method ruleSet-class setDefaultLists setDefaultLists,ruleSet-method setDefaultParams setDefaultParams,ruleSet-method setParams setParams,ruleSet,numeric,numeric,numeric,numeric,numeric,numeric,character,character-method show,ruleSet-method
xsAnnotate constructor for an provided xcmsSet objectxsAnnotate
Class xsAnnotate, a class for annotated peak datashow,xsAnnotate-method xsAnnotate-class