quantMSImageR
This is the development version of quantMSImageR; to use it, please install the devel version of Bioconductor.
Processing and Quantification of Targeted Mass Spectrometry Imaging Data
Bioconductor version: Development (3.24)
Implements tools for processing and quantifying targeted DESI-MRM mass spectrometry imaging (MSI) datasets, extending the Cardinal package. Includes signal-to-noise filtering against background pixels, tissue/background separation, per-feature ion images, quantile heatmaps, quantification against on-slide or on-tissue calibration standards, and batch export of per-feature text images for external viewers.
Author: Matthew J. Smith [aut, cre] 
Maintainer: Matthew J. Smith <mattyjsmith123 at gmail.com>
citation("quantMSImageR")):Matthew J. Smith. quantMSImageR: Processing and Quantification of Targeted Mass Spectrometry Imaging Data. doi:10.18129/B9.bioc.quantMSImageR, R package version 0.99.9, https://bioconductor.org/packages/quantMSImageR.
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("quantMSImageR")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("quantMSImageR")| 2. Quantification with calibration standards | HTML | R Script |
| 1. Introduction to quantMSImageR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ImagingMassSpectrometry, Lipidomics, MassSpectrometry, Metabolomics, Normalization, QualityControl, Software, Visualization |
| Version | 0.99.9 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0), Cardinal (>= 3.6.2) |
| Imports | methods, stats, utils, grDevices, grid, chemCal (>= 0.2.3), viridis (>= 0.6.5), ComplexHeatmap (>= 2.20.0), circlize (>= 0.4.15), pracma (>= 2.4.0), rmarkdown (>= 2.20), purrr (>= 1.0.0), CardinalIO (>= 1.0.0), ProtGenerics (>= 1.34.0), dplyr (>= 1.1.4), ggplot2 (>= 4.0.0), tibble (>= 3.2.1), tidyr (>= 1.3.1), patchwork (>= 1.2.0), yaml (>= 2.3.0) |
| System Requirements | |
| URL | https://mjs-708.github.io/quantMSImageR https://github.com/MJS-708/quantMSImageR |
| Bug Reports | https://github.com/MJS-708/quantMSImageR/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr (>= 1.40), BiocStyle (>= 2.28.0), rstudioapi (>= 0.15.0), DT (>= 0.33), htmltools (>= 0.5.0), magick (>= 2.8.4), openxlsx (>= 4.2.0), matter (>= 2.0.0) |
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| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | quantMSImageR_0.99.9.tar.gz |
| Windows Binary (x86_64) | quantMSImageR_0.99.9.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | quantMSImageR_0.99.9.tgz |
| macOS Binary (sonoma-arm64) | quantMSImageR_0.99.9.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/quantMSImageR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/quantMSImageR |
| Package Short Url | https://bioconductor.org/packages/quantMSImageR/ |
| Package Downloads Report | Download Stats |