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 (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.6.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 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
| 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_1.6.0.tar.gz |
| Windows Binary (x86_64) | squallms_1.6.0.zip |
| macOS Binary (big-sur-x86_64) | squallms_1.6.0.tgz |
| macOS Binary (sonoma-arm64) | squallms_1.6.0.tgz |
| 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 |