{ "_id": "6a1ae7691d7bb097a09f10f5", "Package": "pmp", "Type": "Package", "Title": "Peak Matrix Processing and signal batch correction for\nmetabolomics datasets", "Version": "1.25.0", "Authors@R": "c(\nperson(\nc(\"Andris\"),\n\"Jankevics\",\nrole=c(\"aut\"),\nemail=\"a.jankevics@bham.ac.uk\"),\nperson(\nc(\"Gavin\",\"Rhys\"),\n\"Lloyd\",\nrole=c(\"aut\",\"cre\"),\nemail=\"g.r.lloyd@bham.ac.uk\"),\nperson(\nc(\"Ralf\",\"Johannes\", \"Maria\"),\n\"Weber\",\nrole=c(\"aut\"),\nemail=\"r.j.weber@bham.ac.uk\")\n)", "Maintainer@R": "c( person( c(\"Gavin\",\"Rhys\"), \"Lloyd\",\nrole=c(\"aut\",\"cre\"), email=\"g.r.lloyd@bham.ac.uk\") )", "Description": "Methods and tools for (pre-)processing of metabolomics\ndatasets (i.e. peak matrices), including filtering,\nnormalisation, missing value imputation, scaling, and signal\ndrift and batch effect correction methods. Filtering methods\nare based on: the fraction of missing values (across samples or\nfeatures); Relative Standard Deviation (RSD) calculated from\nthe Quality Control (QC) samples; the blank samples.\nNormalisation methods include Probabilistic Quotient\nNormalisation (PQN) and normalisation to total signal\nintensity. A unified user interface for several commonly used\nmissing value imputation algorithms is also provided. Supported\nmethods are: k-nearest neighbours (knn), random forests (rf),\nBayesian PCA missing value estimator (bpca), mean or median\nvalue of the given feature and a constant small value. The\ngeneralised logarithm (glog) transformation algorithm is\navailable to stabilise the variance across low and high\nintensity mass spectral features. Finally, this package\nprovides an implementation of the Quality Control-Robust Spline\nCorrection (QCRSC) algorithm for signal drift and batch effect\ncorrection of mass spectrometry-based datasets.", "License": "GPL-3", "biocViews": "MassSpectrometry, Metabolomics, Software, QualityControl,\nBatchEffect", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "Collate": "'checkPeakMatrix.R' 'utils.R' 'data.R' 'filters.R'\n'glog_transformation.R' 'mv_imputation.R' 'normalisation.R'\n'sbc_main.R' 'sbc_methods.R' 'sbc_plot.R'", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:51:40 UTC", "RemoteUrl": "https://github.com/bioc/pmp", "RemoteRef": "HEAD", "RemoteSha": "4c5bf37b8896a6fd3fb6269da3418fa979574df5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:36:59 UTC", "User": "root" }, "Author": "Andris Jankevics [aut],\nGavin Rhys Lloyd [aut, cre],\nRalf 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