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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-4.7)RAMClustR_1.3.1.zip(r-4.6)RAMClustR_1.3.1.zip(r-4.5)
RAMClustR_1.3.1.tgz(r-4.6-any)RAMClustR_1.3.1.tgz(r-4.5-any)
RAMClustR_1.3.1.tar.gz(r-4.7-any)RAMClustR_1.3.1.tar.gz(r-4.6-any)
RAMClustR_1.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
RAMClustR/json (API)

# Install 'RAMClustR' in R:

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

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

On CRAN:

massspectrometry metabolomics

6.06 score 13 stars 22 scripts 79 downloads 11 mentions 67 exports 59 dependencies

Last updated from:e005614d80. Checks:7 ERROR, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	ERROR	232
source / vignettes	OK	285
linux-release-x86_64	ERROR	221
macos-release-arm64	ERROR	143
macos-oldrel-arm64	ERROR	123
windows-devel	ERROR	165
windows-release	ERROR	151
windows-oldrel	ERROR	151
wasm-release	OK	220

Exports:adap.to.rc add_params annotate annotation.summary assign.z change.annotation cmpd.summary compute_do.sets compute_SpecAbundAve compute_wt_mean create_ramclustObj define_samples defineExperiment do.findmain export.msfinder.formulas exportDataset filter_blanks filter_good_features filter_signal find_good_features findfeature findmass fooddb2msfinder get_ExpDes get_instrument_platform get.taxon.cids getData getSmilesInchi import.adap.kdb import.msfinder.formulas import.msfinder.mssearch import.msfinder.structures import.sirius impRamSearch manual.annotation.template mean_signal_intensities mergeRCobjects ramclustR rc.calibrate.ri rc.cmpd.filter.blanks rc.cmpd.filter.cv rc.cmpd.get.classyfire rc.cmpd.get.pubchem rc.cmpd.get.smiles.inchi rc.cmpd.replace.na rc.expand.sample.names rc.export.msp.rc rc.feature.filter.blanks rc.feature.filter.cv rc.feature.normalize.batch.qc rc.feature.normalize.qc rc.feature.normalize.quantile rc.feature.normalize.tic rc.feature.replace.na rc.get.csv.data rc.get.df.data rc.get.xcms.data rc.qc rc.ramclustr rc.remove.qc rc.restore.qc.samples RCQC remove_blanks replace_na write_csv write.methods write.msp

Dependencies:askpass base64enc Biobase BiocGenerics bit bitops caTools class cli cpp11 curl data.tree dplyr dynamicTreeCut e1071 farver fastcluster ff generics ggplot2 glue gplots gtable gtools httr isoband jsonlite KernSmooth labeling lifecycle magrittr MASS mime openssl pcaMethods pillar pkgconfig preprocessCore proxy purrr R6 RColorBrewer Rcpp rlang rvest S7 scales selectr stringi stringr sys tibble tidyselect utf8 vctrs viridisLite webchem withr xml2

RAMClustR

Rendered fromRAMClustR.Rmdusingknitr::rmarkdown

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

Help page	Topics
adap.to.rc	adap.to.rc
add_params	add_params
evaluate ramSearch, MSFinder mssearch, MSFinder Structure, MSFinder Formula, and findmain output to annotate spectra of ramclustR object	annotate
annotation.summary()	annotation.summary
assign.z	assign.z
evaluate ramSearch, MSFinder mssearch, MSFinder Structure, MSFinder Formula, and findmain output to annotate spectra of ramclustR object	change.annotation
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
cmpd.summary	cmpd.summary
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
do.findmain	do.findmain
export MSFinder formula prediction results in tabular format.	export.msfinder.formulas
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
foodb2msfinder	fooddb2msfinder
get_ExpDes	get_ExpDes
get_instrument_platform	get_instrument_platform
get.taxon.cids	get.taxon.cids
getData	getData
getSmilesInchi	getSmilesInchi
import.adap.kdb	import.adap.kdb
import.msfinder.formulas	import.msfinder.formulas
import.MSFinder.mssearch	import.msfinder.mssearch
write.methods	import.msfinder.structures
import.sirius	import.sirius
impRamSearch	impRamSearch
manual.annotation.template	manual.annotation.template
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
getClassyFire	rc.cmpd.get.classyfire
rc.cmpd.get.pubchem	rc.cmpd.get.pubchem
getSmilesInchi	rc.cmpd.get.smiles.inchi
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.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.methods	write.methods
write.msp	write.msp

Package: RAMClustR 1.3.1

RAMClustR: Mass Spectrometry Metabolomics Feature Clustering and Interpretation

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