MRManalyzeR
This is the development version of MRManalyzeR; to use it, please install the devel version of Bioconductor.
Process and Analyse Targeted LC-MS Lipidomics and Metabolomics Data
Bioconductor version: Development (3.24)
Reproducible post-acquisition processing of targeted LC-MS/MS lipidomics and metabolomics results exported from Waters TargetLynx or from Skyline, or supplied as a plain sample-by-analyte matrix. Reads the quantitative result tables, integrates them with sample and feature metadata, and applies configurable signal filtering (SNR, LOD or LOQ), blank filtering, batch correction, normalisation, internal-standard and volume adjustment of vendor-reported concentrations, and missing-value imputation. Each step is an exported function acting on a struct DatasetExperiment; a complete workflow can additionally be driven from a single YAML configuration via runMRManalyzeR(), which also renders self-contained HTML data-quality and statistical reports. Chromatographic peak detection, peak integration and calibration-curve fitting from raw mass-spectrometry data are outside its scope.
Author: Matthew J. Smith [aut, cre] 
, Antonio Checa [aut]
Maintainer: Matthew J. Smith <mattyjsmith123 at gmail.com>
citation("MRManalyzeR")):Matthew J. Smith, Antonio Checa. MRManalyzeR: Process and Analyse Targeted LC-MS Lipidomics and Metabolomics Data. doi:10.18129/B9.bioc.MRManalyzeR, R package version 0.99.8, https://bioconductor.org/packages/MRManalyzeR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("MRManalyzeR")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("MRManalyzeR")| Getting started with MRManalyzeR | HTML | R Script |
| Processing in detail | HTML | R Script |
| Reference Manual |
Details
| biocViews | BatchEffect, Lipidomics, MassSpectrometry, Metabolomics, Normalization, QualityControl, Software, Visualization, WorkflowStep |
| Version | 0.99.8 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0), struct |
| Imports | dplyr, tidyr, tibble, yaml, openxlsx, janitor, rmarkdown, methods, ggplot2, ggnewscale, rlang, grDevices, pheatmap, withr, DT, stats, utils |
| System Requirements | |
| URL | https://github.com/MJS-708/MRManalyzeR |
| Bug Reports | https://github.com/MJS-708/MRManalyzeR/issues |
See More
| Suggests | pmp, structToolbox, pls, SummarizedExperiment, ggrepel, plotly, htmltools, knitr, cowplot, gridExtra, BiocStyle, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MRManalyzeR_0.99.8.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/MRManalyzeR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MRManalyzeR |
| Package Short Url | https://bioconductor.org/packages/MRManalyzeR/ |
| Package Downloads Report | Download Stats |