Package: RAMClustR 1.3.0
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 2 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 |