Package: squallms 0.99.6
squallms: Speedy quality assurance via lasso labeling for LC-MS data
squallms is a Bioconductor R package that implements a "semi-labeled" approach to untargeted mass spectrometry data. It pulls in raw data from mass-spec files to calculate several metrics that are then used to label MS features in bulk as high or low quality. These metrics of peak quality are then passed to a simple logistic model that produces a fully-labeled dataset suitable for downstream analysis.
Authors:
squallms_0.99.6.tar.gz
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squallms.pdf |squallms.html✨
squallms/json (API)
NEWS
# Install 'squallms' in R: |
install.packages('squallms', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/wkumler/squallms/issues
On BioConductor:squallms-0.99.6(bioc 3.20)
Last updated 1 months agofrom:defbc6a84a
Exports:extractChromMetricslabelFeatsLassolabelFeatsManuallogModelFeatProblogModelFeatQualitymakeXcmsObjFlatpickyPCAupdateXcmsObjFeats
Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbslibcachemcaretclasscliclockclueclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydiagramdigestdoParalleldplyre1071ellipsisevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2globalsgluegowergtablehardhathighrhmshtmltoolshtmlwidgetshttpuvhttrigraphimputeipredIRangesisobanditeratorsjquerylibjsonliteKernSmoothkeysknitrlabelinglambda.rlaterlatticelavalazyevallifecyclelimmalistenvlubridatemagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeModelMetricsMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmennetnumDerivopensslparallellypcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitspROCprodlimprogressprogressrpromisesProtGenericsproxyPSMatchpurrrQFeaturesR6RaMSrappdirsRColorBrewerRcpprecipesreshape2Rhdf5librlangrmarkdownrpartS4ArraysS4VectorssassscalesshapeshinysnowsourcetoolsSparseArraySpectraSQUAREMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimechangetimeDatetinytextzdbUCSC.utilsutf8vctrsviridisLitevsnwithrxcmsxfunXMLxml2xtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Extract metrics of chromatographic peak quality | extractChromMetrics |
Label similar chromatographic features in bulk via interactive selection | labelFeatsLasso |
Label chromatographic features manually one at a time via interactive interface | labelFeatsManual |
Model feature quality using a logistic regression | logModelFeatProb |
Turn 0-1 likelihood values into categorical (good/bad) classifications | logModelFeatQuality |
Make an XCMS object flat | makeXcmsObjFlat |
Perform a PCA on multi-file chromatographic data | pickyPCA |
Update features in an XCMS object | updateXcmsObjFeats |