Package: squallms 1.7.0

William Kumler

squallms: Speedy quality assurance via lasso labeling for LC-MS data

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.

Authors:William Kumler [aut, cre, cph]

squallms_1.7.0.tar.gz
squallms_1.7.0.zip(r-4.7)squallms_1.7.0.zip(r-4.6)squallms_1.7.0.zip(r-4.5)
squallms_1.7.0.tgz(r-4.6-any)squallms_1.7.0.tgz(r-4.5-any)
squallms_1.7.0.tar.gz(r-4.7-any)squallms_1.7.0.tar.gz(r-4.6-any)
squallms_1.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
squallms/json (API)

# Install 'squallms' in R:

install.packages('squallms', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wkumler/squallms/issues

On BioConductor:squallms-1.7.0(bioc 3.24)squallms-1.6.0(bioc 3.23)

massspectrometry metabolomics proteomics lipidomics shinyapps classification clustering featureextraction principalcomponent regression preprocessing qualitycontrol visualization

4.48 score 3 stars 7 scripts 235 downloads 8 exports 176 dependencies

Last updated from:454253cb01. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	234
linux-devel-x86_64	OK	538
source / vignettes	OK	353
linux-release-x86_64	OK	606
macos-release-arm64	OK	323
macos-oldrel-arm64	OK	299
windows-devel	OK	485
windows-release	OK	483
windows-oldrel	OK	564
wasm-release	OK	189

Exports:extractChromMetrics labelFeatsLasso labelFeatsManual logModelFeatProb logModelFeatQuality makeXcmsObjFlat pickyPCA updateXcmsObjFeats

Dependencies:abind affy affyio AnnotationFilter askpass base64enc BH Biobase BiocBaseUtils BiocGenerics biocmake BiocManager BiocParallel bslib cachem caret class cli clock clue cluster codetools commonmark cpp11 crayon crosstalk curl data.table DBI DelayedArray diagram digest dir.expiry doParallel dplyr e1071 evaluate farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options future future.apply generics GenomicRanges ggplot2 globals glue gower gtable hardhat highr hms htmltools htmlwidgets httpuv httr igraph impute ipred IRanges isoband iterators jquerylib jsonlite KernSmooth keys knitr labeling lambda.r later lattice lava lazyeval lifecycle limma listenv lubridate magrittr MALDIquant MASS MassSpecWavelet Matrix MatrixGenerics matrixStats memoise MetaboCoreUtils mime ModelMetrics MsCoreUtils MsExperiment MsFeatures MSnbase MultiAssayExperiment mzID mzR ncdf4 nlme nnet numDeriv openssl otel parallelly pcaMethods pillar pkgconfig plotly plyr preprocessCore prettyunits pROC prodlim progress progressr promises ProtGenerics proxy PSMatch PTMods purrr QFeatures R6 RaMS rappdirs RColorBrewer Rcpp recipes reshape2 Rhdf5lib rlang rmarkdown rpart S4Arrays S4Vectors S7 sass scales Seqinfo shape shiny snow sourcetools SparseArray sparsevctrs Spectra SQUAREM statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timechange timeDate tinytex tzdb utf8 vctrs viridisLite vsn withr xcms xfun XML xml2 xtable XVector yaml

Introduction to squallms

Rendered fromintro_to_squallms.Rmdusingknitr::rmarkdown

Last update: 2024-06-07
Started: 2024-03-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Extract metrics of chromatographic peak quality	extractChromMetrics
Label similar chromatographic features in bulk via interactive selection	labelFeatsLasso
Label chromatographic features manually one at a time via interactive interface	labelFeatsManual
Model feature quality using a logistic regression	logModelFeatProb
Turn 0-1 likelihood values into categorical (good/bad) classifications	logModelFeatQuality
Make an XCMS object flat	makeXcmsObjFlat
Perform a PCA on multi-file chromatographic data	pickyPCA
Update features in an XCMS object	updateXcmsObjFeats