Package: RAMClustR 1.3.1

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 data <doi:10.1021/ac501530d>.

Authors:Corey D. Broeckling [aut], Fayyaz Afsar [aut], Steffen Neumann [aut], Asa Ben-Hur [aut], Jessica Prenni [aut], Helge Hecht [cre], Matej Trojak [ctb], Zargham Ahmad [ctb]

RAMClustR_1.3.1.tar.gz
RAMClustR_1.3.1.zip(r-4.5)RAMClustR_1.3.1.zip(r-4.4)RAMClustR_1.3.1.zip(r-4.3)
RAMClustR_1.3.1.tgz(r-4.4-any)RAMClustR_1.3.1.tgz(r-4.3-any)
RAMClustR_1.3.1.tar.gz(r-4.5-noble)RAMClustR_1.3.1.tar.gz(r-4.4-noble)
RAMClustR_1.3.1.tgz(r-4.4-emscripten)RAMClustR_1.3.1.tgz(r-4.3-emscripten)
RAMClustR.pdf |RAMClustR.html✨
RAMClustR/json (API)

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

Peer review:

Bug tracker:https://github.com/cbroeckl/ramclustr/issues

On CRAN:

massspectrometrymetabolomics

6.86 score 12 stars 20 scripts 313 downloads 11 mentions 67 exports 64 dependencies

Last updated 1 years agofrom:e005614d80 (on e005614d808e0ca93c459ec8cc103b87cd5d11fd). Checks:OK: 1 ERROR: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winERRORNov 20 2024
R-4.5-linuxERRORNov 20 2024
R-4.4-winERRORNov 20 2024
R-4.4-macERRORNov 20 2024
R-4.3-winERRORNov 20 2024
R-4.3-macERRORNov 20 2024

Exports:adap.to.rcadd_paramsannotateannotation.summaryassign.zchange.annotationcmpd.summarycompute_do.setscompute_SpecAbundAvecompute_wt_meancreate_ramclustObjdefine_samplesdefineExperimentdo.findmainexport.msfinder.formulasexportDatasetfilter_blanksfilter_good_featuresfilter_signalfind_good_featuresfindfeaturefindmassfooddb2msfinderget_ExpDesget_instrument_platformget.taxon.cidsgetDatagetSmilesInchiimport.adap.kdbimport.msfinder.formulasimport.msfinder.mssearchimport.msfinder.structuresimport.siriusimpRamSearchmanual.annotation.templatemean_signal_intensitiesmergeRCobjectsramclustRrc.calibrate.rirc.cmpd.filter.blanksrc.cmpd.filter.cvrc.cmpd.get.classyfirerc.cmpd.get.pubchemrc.cmpd.get.smiles.inchirc.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.qcrc.ramclustrrc.remove.qcrc.restore.qc.samplesRCQCremove_blanksreplace_nawrite_csvwrite.methodswrite.msp

Dependencies:askpassbase64encBiobaseBiocGenericsbitbitopscaToolsclassclicolorspacecurldata.treedplyrdynamicTreeCute1071fansifarverfastclusterffgenericsggplot2gluegplotsgtablegtoolshttrisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpcaMethodspillarpkgconfigpreprocessCoreproxypurrrR6RColorBrewerRcpprlangrvestscalesselectrstringistringrsystibbletidyselectutf8vctrsviridisLitewebchemwithrxml2

RAMClustR

Corey Broeckling

Rendered fromRAMClustR.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2023-05-17
Started: 2017-09-26

Readme and manuals

Help Manual

Help pageTopics
adap.to.rcadap.to.rc
add_paramsadd_params
evaluate ramSearch, MSFinder mssearch, MSFinder Structure, MSFinder Formula, and findmain output to annotate spectra of ramclustR objectannotate
annotation.summary()annotation.summary
assign.zassign.z
evaluate ramSearch, MSFinder mssearch, MSFinder Structure, MSFinder Formula, and findmain output to annotate spectra of ramclustR objectchange.annotation
check_arguments_filter.blankscheck_arguments_filter.blanks
check_arguments_filter.cvcheck_arguments_filter.cv
check_arguments_replace.nacheck_arguments_replace.na
checkschecks
cmpd.summarycmpd.summary
compute_do.setscompute_do.sets
compute_SpecAbundAvecompute_SpecAbundAve
compute_wt_meancompute_wt_mean
create_ramclustObjcreate_ramclustObj
define_samplesdefine_samples
defineExperimentdefineExperiment
do.findmaindo.findmain
export MSFinder formula prediction results in tabular format.export.msfinder.formulas
exportDatasetexportDataset
filter_blanksfilter_blanks
filter_good_featuresfilter_good_features
filter_signalfilter_signal
find_good_featuresfind_good_features
findfeaturefindfeature
findmassfindmass
foodb2msfinderfooddb2msfinder
get_ExpDesget_ExpDes
get_instrument_platformget_instrument_platform
get.taxon.cidsget.taxon.cids
getDatagetData
getSmilesInchigetSmilesInchi
import.adap.kdbimport.adap.kdb
import.msfinder.formulasimport.msfinder.formulas
import.MSFinder.mssearchimport.msfinder.mssearch
write.methodsimport.msfinder.structures
import.siriusimport.sirius
impRamSearchimpRamSearch
manual.annotation.templatemanual.annotation.template
mean_signal_intensitiesmean_signal_intensities
mergeRCobjectsmergeRCobjects
normalized_data_batch_qcnormalized_data_batch_qc
normalized_data_ticnormalized_data_tic
order_datasetsorder_datasets
ramclustRramclustR
rc.calibrate.rirc.calibrate.ri
rc.cmpd.filter.blanksrc.cmpd.filter.blanks
rc.cmpd.filter.cvrc.cmpd.filter.cv
getClassyFirerc.cmpd.get.classyfire
rc.cmpd.get.pubchemrc.cmpd.get.pubchem
getSmilesInchirc.cmpd.get.smiles.inchi
rc.cmpd.replace.narc.cmpd.replace.na
rc.expand.sample.namesrc.expand.sample.names
rc.export.msp.rcrc.export.msp.rc
rc.feature.filter.blanksrc.feature.filter.blanks
rc.feature.filter.cvrc.feature.filter.cv
rc.feature.normalize.batch.qcrc.feature.normalize.batch.qc
rc.feature.normalize.qcrc.feature.normalize.qc
rc.feature.normalize.quantilerc.feature.normalize.quantile
rc.feature.normalize.ticrc.feature.normalize.tic
rc.feature.replace.narc.feature.replace.na
rc.get.csv.datarc.get.csv.data
rc.get.df.datarc.get.df.data
rc.get.xcms.datarc.get.xcms.data
rc.qcrc.qc
rc.ramclustrrc.ramclustr
rc.remove.qcrc.remove.qc
rc.restore.qc.samplesrc.restore.qc.samples
RCQCRCQC
remove_blanksremove_blanks
replace_nareplace_na
write_csvwrite_csv
write.methodswrite.methods
write.mspwrite.msp