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Bioconductor - squallms

squallms

This is the released version of squallms; for the devel version, see squallms.

Speedy quality assurance via lasso labeling for LC-MS data

Bioconductor version: Release (3.21)

squallms is a Bioconductor R package that implements a "semi-labeled" approach to untargeted mass spectrometry data. It pulls in raw data from mass-spec files to calculate several metrics that are then used to label MS features in bulk as high or low quality. These metrics of peak quality are then passed to a simple logistic model that produces a fully-labeled dataset suitable for downstream analysis.

Author: William Kumler [aut, cre, cph] ORCID: 0000-0002-5022-8009

Maintainer: William Kumler <wkumler at uw.edu>

Citation (from within R, enter citation("squallms")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("squallms")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("squallms")

Details biocViews Classification, Clustering, FeatureExtraction, Lipidomics, MassSpectrometry, Metabolomics, Preprocessing, PrincipalComponent, Proteomics, QualityControl, Regression, ShinyApps, Software, Visualization Version 1.2.0 In Bioconductor since BioC 3.20 (R-4.4) (0.5 years) License MIT + file LICENSE Depends R (>= 4.1.0) Imports xcms, MSnbase, MsExperiment, RaMS, dplyr, tidyr, tibble, ggplot2, shiny, plotly, data.table, caret, stats, graphics, utils, keys System Requirements URL https://github.com/wkumler/squallms Bug Reports https://github.com/wkumler/squallms/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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