Package: RAMClustR 1.3.0
Helge Hecht
RAMClustR: Mass Spectrometry Metabolomics Feature Clustering and Interpretation
A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. This method is compatible with gas and liquid chromatography coupled mass spectrometry, including indiscriminant tandem mass spectrometry <doi:10.1021/ac501530d> data.
Authors:
RAMClustR_1.3.0.tar.gz
RAMClustR_1.3.0.tar.gz(r-4.4-noble)
RAMClustR_1.3.0.tgz(r-4.4-emscripten)RAMClustR_1.3.0.tgz(r-4.3-emscripten)
RAMClustR.pdf |RAMClustR.html✨
RAMClustR/json (API)
| # Install 'RAMClustR' in R: |
| install.packages('RAMClustR', repos = c('https://cbroeckl.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cbroeckl/ramclustr/issues
Last updated 3 months agofrom:5f0adcb2af. Checks:OK: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 27 2024 |
Exports:add_paramscompute_do.setscompute_SpecAbundAvecompute_wt_meancreate_ramclustObjdefine_samplesdefineExperimentdoFindmainexportDatasetfilter_blanksfilter_good_featuresfilter_signalfind_good_featuresfindfeaturefindmassget_ExpDesget_instrument_platformgetDatamean_signal_intensitiesmergeRCobjectsramclustRrc.calibrate.rirc.cmpd.filter.blanksrc.cmpd.filter.cvrc.cmpd.replace.narc.expand.sample.namesrc.export.msp.rcrc.feature.filter.blanksrc.feature.filter.cvrc.feature.normalize.batch.qcrc.feature.normalize.qcrc.feature.normalize.quantilerc.feature.normalize.ticrc.feature.replace.narc.get.csv.datarc.get.df.datarc.get.xcms.datarc.merge.split.clustersrc.qcrc.ramclustrrc.remove.qcrc.restore.qc.samplesRCQCremove_blanksreplace_nawrite_csvwrite.gcei.matwrite.methodswrite.msp
Dependencies:BiobaseBiocGenericsbitopscaToolsclassclicolorspacedynamicTreeCute1071enviPatfansifarverfastclusterggplot2gluegplotsgtablegtoolsInterpretMSSpectrumisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepcaMethodspillarpkgconfigplyrpreprocessCoreproxyR6RColorBrewerRcpprlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| add_params | add_params |
| check_arguments_filter.blanks | check_arguments_filter.blanks |
| check_arguments_filter.cv | check_arguments_filter.cv |
| check_arguments_replace.na | check_arguments_replace.na |
| checks | checks |
| compute_do.sets | compute_do.sets |
| compute_SpecAbundAve | compute_SpecAbundAve |
| compute_wt_mean | compute_wt_mean |
| create_ramclustObj | create_ramclustObj |
| define_samples | define_samples |
| defineExperiment | defineExperiment |
| doFindmain | doFindmain |
| exportDataset | exportDataset |
| filter_blanks | filter_blanks |
| filter_good_features | filter_good_features |
| filter_signal | filter_signal |
| find_good_features | find_good_features |
| findfeature | findfeature |
| findmass | findmass |
| get_ExpDes | get_ExpDes |
| get_instrument_platform | get_instrument_platform |
| getData | getData |
| mean_signal_intensities | mean_signal_intensities |
| mergeRCobjects | mergeRCobjects |
| normalized_data_batch_qc | normalized_data_batch_qc |
| normalized_data_tic | normalized_data_tic |
| order_datasets | order_datasets |
| ramclustR | ramclustR |
| rc.calibrate.ri | rc.calibrate.ri |
| rc.cmpd.filter.blanks | rc.cmpd.filter.blanks |
| rc.cmpd.filter.cv | rc.cmpd.filter.cv |
| rc.cmpd.replace.na | rc.cmpd.replace.na |
| rc.expand.sample.names | rc.expand.sample.names |
| rc.export.msp.rc | rc.export.msp.rc |
| rc.feature.filter.blanks | rc.feature.filter.blanks |
| rc.feature.filter.cv | rc.feature.filter.cv |
| rc.feature.normalize.batch.qc | rc.feature.normalize.batch.qc |
| rc.feature.normalize.qc | rc.feature.normalize.qc |
| rc.feature.normalize.quantile | rc.feature.normalize.quantile |
| rc.feature.normalize.tic | rc.feature.normalize.tic |
| rc.feature.replace.na | rc.feature.replace.na |
| rc.get.csv.data | rc.get.csv.data |
| rc.get.df.data | rc.get.df.data |
| rc.get.xcms.data | rc.get.xcms.data |
| rc.merge.split.clusters | rc.merge.split.clusters |
| rc.qc | rc.qc |
| rc.ramclustr | rc.ramclustr |
| rc.remove.qc | rc.remove.qc |
| rc.restore.qc.samples | rc.restore.qc.samples |
| RCQC | RCQC |
| remove_blanks | remove_blanks |
| replace_na | replace_na |
| write_csv | write_csv |
| write.gcei.mat | write.gcei.mat |
| write.methods | write.methods |
| write.msp | write.msp |
