Package: MSstatsQC 2.29.3

Eralp Dogu

MSstatsQC: Longitudinal system suitability monitoring and quality control for proteomic experiments

MSstatsQC is an R package which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments.

Authors:Eralp Dogu [aut, cre], Sara Taheri [aut], Olga Vitek [aut]

MSstatsQC_2.29.3.tar.gz
MSstatsQC_2.29.3.zip(r-4.7)MSstatsQC_2.29.3.zip(r-4.6)MSstatsQC_2.29.3.zip(r-4.5)
MSstatsQC_2.29.3.tgz(r-4.6-any)MSstatsQC_2.29.3.tgz(r-4.5-any)
MSstatsQC_2.29.3.tar.gz(r-4.6-any)MSstatsQC_2.29.3.tar.gz(r-4.5-any)
MSstatsQC_2.29.3.tgz(r-4.5-emscripten)
MSstatsQC.pdf |MSstatsQC.html✨
MSstatsQC/json (API)
NEWS

# Install 'MSstatsQC' in R:

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

Datasets:

QCloudDDA - DDA QC data from QCloud System
QCloudSRM - SRM QC data from QCloud System
QuiCDIA - DIA iRT data from QuiC System
S9Site54 - CPTAC study 9.1 site 54 dataset

On BioConductor:MSstatsQC-2.29.3(bioc 3.23)MSstatsQC-2.28.0(bioc 3.22)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software qualitycontrol proteomics massspectrometry normalization

4.65 score 1 packages 8 scripts 386 downloads 1 mentions 14 exports 187 dependencies

Last updated from:0c558091dc. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	271
linux-devel-x86_64	WARNING	433
source / vignettes	OK	488
linux-release-x86_64	WARNING	501
macos-release-arm64	WARNING	308
macos-oldrel-arm64	WARNING	247
windows-devel	WARNING	539
windows-release	WARNING	521
windows-oldrel	WARNING	576
wasm-release	OK	250

Exports:ChangePointEstimator CUSUMChart DataProcess DecisionMap MissingDataMap MSnbaseToMSstatsQC MSstatsQC.ML.deployR MSstatsQC.ML.sim.size.detectR MSstatsQC.ML.trainR mzQCToMSstatsQC RadarPlot RemoveMissing RiverPlot XmRChart

Dependencies:abind affy affyio AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics biocmake BiocManager BiocParallel bitops boot broom bslib cachem car carData cli clue cluster codetools colorspace colourpicker combinat commonmark conf.design cowplot cpp11 crosstalk curl data.table DelayedArray Deriv digest dir.expiry doBy DoE.base doParallel dplyr evaluate farver fastmap filelock fontawesome foreach forecast formatR Formula fracdiff FrF2 fs futile.logger futile.options generics GenomicRanges ggExtra ggplot2 glue gmp gtable h2o highr htmltools htmlwidgets httpuv httr igraph impute IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle limma lme4 lmtest magrittr MALDIquant MASS Matrix MatrixGenerics MatrixModels matrixStats memoise MetaboCoreUtils mgcv microbenchmark mime miniUI minqa modelr MsCoreUtils MSnbase MultiAssayExperiment mzID mzR ncdf4 nlme nloptr nnet numbers numDeriv openssl otel pander partitions pbkrtest pcaMethods pillar pkgconfig plotly plyr polynom preprocessCore promises ProtGenerics PSMatch PTMods purrr qcmetrics QFeatures quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack reformulas reshape2 Rhdf5lib rlang rmarkdown S4Arrays S4Vectors S7 sass scales scatterplot3d Seqinfo sets sfsmisc shiny shinyjs snow sourcetools SparseArray SparseM Spectra statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate tinytex urca utf8 vcd vctrs viridisLite vsn withr xfun XML xtable XVector yaml zoo

Longitudinal System Suitability Monitoring and Quality Control with MSstatsQC

Eralp Dogu [email protected], Sara Taheri [email protected], Olga Vitek [email protected]

Rendered fromMSstatsQC.Rmdusingknitr::rmarkdownon Apr 09 2026.

Last update: 2026-02-07
Started: 2017-06-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A function to identify the time of a change in the mean or variability of a metric	ChangePointEstimator
A function to create cumulative sum charts for mean (CUSUMm) and cumulative sum charts for variability (CUSUMv) control charts	CUSUMChart
A data processing function	DataProcess
A function to create heatmaps to compare performance with user defined performance criteria	DecisionMap
A function to summarize missing values	MissingDataMap
A function to convert MSnbase files to MSstatsQC format	MSnbaseToMSstatsQC
A function to test random forest classifiers for QC data	MSstatsQC.ML.deployR
A function to train random forest classifiers for QC data	MSstatsQC.ML.sim.size.detectR
A function to train random forest classifiers for QC data	MSstatsQC.ML.trainR
A function to convert mzQC files to MSstatsQC format	mzQCToMSstatsQC
DDA QC data from QCloud System	QCloudDDA
SRM QC data from QCloud System	QCloudSRM
DIA iRT data from QuiC System	QuiCDIA
A function to create radar plot to aggregate results from X and mR charts or CUSUMm and CUSUMv charts.	RadarPlot
A data processing function for removing missing values	RemoveMissing
A function to create river plot to aggregate results from X and mR charts or CUSUMm and CUSUMv charts.	RiverPlot
CPTAC study 9.1 site 54 dataset	S9Site54
A function to construct individual (X) and moving range (mR) control charts	XmRChart