Package: MetabolomicsBasics 1.5.1

MetabolomicsBasics: Basic Functions to Investigate Metabolomics Data Matrices

A set of functions to investigate raw data from (metabol)omics experiments intended to be used on a raw data matrix, i.e. following peak picking and signal deconvolution. Functions can be used to normalize data, detect biomarkers and perform sample classification. A detailed description of best practice usage may be found in the publication <doi:10.1007/978-1-4939-7819-9_20>.

Authors:Jan Lisec [aut, cre]

MetabolomicsBasics_1.5.1.tar.gz
MetabolomicsBasics_1.5.1.zip(r-4.7)MetabolomicsBasics_1.5.1.zip(r-4.6)MetabolomicsBasics_1.5.1.zip(r-4.5)
MetabolomicsBasics_1.5.1.tgz(r-4.6-any)MetabolomicsBasics_1.5.1.tgz(r-4.5-any)
MetabolomicsBasics_1.5.1.tar.gz(r-4.7-any)MetabolomicsBasics_1.5.1.tar.gz(r-4.6-any)
MetabolomicsBasics_1.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MetabolomicsBasics/json (API)

# Install 'MetabolomicsBasics' in R:

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

Bug tracker:https://github.com/janlisec/metabolomicsbasics/issues

Uses libs:

openjdk– OpenJDK Java runtime, using Hotspot JIT

Datasets:

met - Metabolite table
raw - Metabolomics data set
sam - Sample table

On CRAN:

openjdk

3.48 score 3 scripts 254 downloads 2 mentions 21 exports 107 dependencies

Last updated from:6e9aa46cd9. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	257
source / vignettes	OK	293
linux-release-x86_64	OK	250
macos-release-arm64	OK	183
macos-oldrel-arm64	OK	226
windows-devel	OK	195
windows-release	OK	207
windows-oldrel	OK	161
wasm-release	OK	164

Exports:AdjustSymbols CheckForOutliers ClassificationCV ClassificationHistogram ClassificationWrapper find_boundaries MBoxplot MetaboliteANOVA msconvert PlotMetabolitePCA PlotPValueHist PolarCoordHeterPlot read_msdial recalib_mzML RemoveFactorsByANOVA ReplaceMissingValues RestrictedPCA spectra_format_converter sumformula_from_CAS unique_labels unique_subformula_masses

Dependencies:askpass base64enc Biobase BiocGenerics C50 caret class cli clock codetools CorrectOverloadedPeaks cpp11 Cubist curl data.table data.tree diagram digest dplyr e1071 enviPat farver fingerprint foreach Formula fs future future.apply generics ggplot2 globals glue gower gtable hardhat HiResTEC httr InterpretMSSpectrum inum ipred isoband iterators itertools jsonlite KernSmooth labeling lattice lava libcoin lifecycle listenv lubridate magrittr MASS Matrix mime ModelMetrics mvtnorm nlme nnet numDeriv openssl parallelly partykit pcaMethods pillar pkgconfig plyr png pROC prodlim progressr proxy purrr R6 rcdk rcdklibs RColorBrewer Rcpp recipes reshape2 rJava rlang rpart rvest S7 scales selectr shape sparsevctrs SQUAREM stringi stringr survival sys tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs viridisLite webchem withr xml2

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
AdjustSymbols.	AdjustSymbols
CheckForOutliers.	CheckForOutliers
ClassificationCV.	ClassificationCV
ClassificationHistogram.	ClassificationHistogram
ClassificationWrapper.	ClassificationWrapper
find_boundaries.	find_boundaries
MBoxplot.	MBoxplot
Metabolite table	met
MetaboliteANOVA.	MetaboliteANOVA
msconvert.	msconvert
PlotMetabolitePCA.	PlotMetabolitePCA
PlotPValueHist.	PlotPValueHist
PolarCoordHeterPlot.	PolarCoordHeterPlot
Metabolomics data set	raw
read_msdial	read_msdial
recalib_mzML	recalib_mzML
RemoveFactorsByANOVA.	RemoveFactorsByANOVA
ReplaceMissingValues.	ReplaceMissingValues
RestrictedPCA.	RestrictedPCA
Sample table	sam
spectra_format_converter.	spectra_format_converter
sumformula_from_CAS.	sumformula_from_CAS
unique_labels.	unique_labels
unique_subformula_masses	unique_subformula_masses