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Package: RAMClustR 1.3.4

Corey D. Broeckling

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. Initially described by Broeckling et all (2014) <doi:10.1021/ac501530d>.

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

RAMClustR_1.3.4.tar.gz
RAMClustR_1.3.4.zip(r-4.7-any)RAMClustR_1.3.4.zip(r-4.6-any)RAMClustR_1.3.4.zip(r-4.5-any)
RAMClustR_1.3.4.tgz(r-4.6-any)RAMClustR_1.3.4.tgz(r-4.5-any)
RAMClustR_1.3.4.tar.gz(r-4.7-any)RAMClustR_1.3.4.tar.gz(r-4.6-any)
RAMClustR_1.3.4.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

7.00 score 13 stars 24 scripts 90 downloads 11 mentions 51 exports 171 dependencies

Last updated from:671f929d7b. Checks:9 OK. Indexed: no.

Target	Result	Time
linux-devel	OK	250
source / vignettes	OK	276
linux-release	OK	249
macos-release	OK	169
macos-oldrel	OK	150
windows-devel	OK	207
windows-release	OK	157
windows-oldrel	OK	165
wasm-release	OK	168

Exports:add_params compute_do.sets compute_SpecAbundAve compute_wt_mean create_ramclustObj define_samples defineExperiment do.findmain exportDataset filter_blanks filter_good_features filter_signal find_good_features findfeature findmass get_ExpDes get_instrument_platform getData getSampleMetadata mean_signal_intensities mergeRCobjects ramclustR rc.calibrate.ri rc.cmpd.filter.blanks rc.cmpd.filter.cv 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.feature.replace.na.mai rc.get.csv.data rc.get.df.data rc.get.xcms.data rc.merge.split.clusters rc.qc rc.ramclustr rc.remove.qc rc.restore.qc.samples RCQC.plots remove_blanks replace_na write_csv write.gcei.mat write.methods write.msp

Dependencies:abind askpass backports base64enc Biobase BiocGenerics bit bit64 bitops blob broom bslib cachem callr caret caTools cellranger class cli clipr clock codetools conflicted cpp11 crayon curl data.table DBI dbplyr DelayedArray diagram digest doParallel doRNG dplyr dtplyr dynamicTreeCut e1071 evaluate farver fastcluster fastmap fontawesome forcats foreach fs future future.apply gargle generics GenomicRanges ggplot2 globals glue googledrive googlesheets4 gower gplots gtable gtools hardhat haven highr hms htmltools httr ids ipred IRanges isoband iterators itertools jquerylib jsonlite KernSmooth knitr labeling lattice lava lifecycle listenv lubridate magrittr MAI MASS Matrix MatrixGenerics matrixStats memoise mime missForest ModelMetrics modelr nlme nnet numDeriv openssl otel parallelly pcaMethods pillar pkgconfig plyr prettyunits pROC processx prodlim progress progressr proxy ps purrr R6 ragg randomForest ranger rappdirs rbibutils RColorBrewer Rcpp RcppEigen Rdpack readr readxl recipes rematch rematch2 reprex reshape2 rlang rmarkdown rngtools rpart rstudioapi rvest S4Arrays S4Vectors S7 sass scales selectr Seqinfo shape SparseArray sparsevctrs SQUAREM stringi stringr SummarizedExperiment survival sys systemfonts textshaping tibble tidyr tidyselect tidyverse timechange timeDate tinytex tzdb utf8 uuid vctrs viridisLite vroom withr xfun xml2 XVector yaml

RAMClustR

Rendered fromRAMClustR.Rmdusingknitr::rmarkdown

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

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
do.findmain	do.findmain
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
Extract Sample Metadata from an xcms Object	getSampleMetadata
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.feature.replace.na.mai	rc.feature.replace.na.mai
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.plots	RCQC.plots
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

Package: RAMClustR 1.3.4

RAMClustR: Mass Spectrometry Metabolomics Feature Clustering and Interpretation

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