squallms

This is the development version of squallms; to use it, please install the devel version of Bioconductor.

Speedy quality assurance via lasso labeling for LC-MS data


Bioconductor version: Development (3.20)

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]

Maintainer: William Kumler <wkumler at uw.edu>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Introduction to squallms HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Classification, Clustering, FeatureExtraction, Lipidomics, MassSpectrometry, Metabolomics, Preprocessing, PrincipalComponent, Proteomics, QualityControl, Regression, ShinyApps, Software, Visualization
Version 0.99.6
In Bioconductor since BioC 3.20 (R-4.4)
License MIT + file LICENSE
Depends R (>= 3.5.0)
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
Suggests knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
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Package Archives

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

Source Package squallms_0.99.6.tar.gz
Windows Binary squallms_0.99.6.zip
macOS Binary (x86_64) squallms_0.99.6.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/squallms
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/squallms
Bioc Package Browser https://code.bioconductor.org/browse/squallms/
Package Short Url https://bioconductor.org/packages/squallms/
Package Downloads Report Download Stats