squallms
Speedy quality assurance via lasso labeling for LC-MS data
Bioconductor version: Release (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("squallms")):
Installation
To install this package, start R (version "4.4") 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")| Introduction to squallms | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, Clustering, FeatureExtraction, Lipidomics, MassSpectrometry, Metabolomics, Preprocessing, PrincipalComponent, Proteomics, QualityControl, Regression, ShinyApps, Software, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (< 6 months) |
| 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | squallms_1.0.0.tar.gz |
| Windows Binary (x86_64) | squallms_1.0.0.zip |
| macOS Binary (x86_64) | |
| 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 |