squallms
This is thereleased version of squallms; for the devel version, seesquallms.
Speedy quality assurance via lasso labeling for LC-MS data
Bioconductor version: Release (3.22)
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("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 appropriateBioconductor 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 | 1.4.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (1 year) |
| License | MIT + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | squallms_1.4.0.tar.gz |
| Windows Binary (x86_64) | squallms_1.4.0.zip |
| macOS Binary (x86_64) | squallms_1.4.0.tgz |
| macOS Binary (arm64) | squallms_1.4.0.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 |