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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| 1. Introduction to quantMSImageR | HTML | R Script |
| 2. Quantification with calibration standards | HTML | R Script |
| Reference Manual |
Details
| biocViews | ImagingMassSpectrometry, Lipidomics, MassSpectrometry, Metabolomics, Normalization, QualityControl, Software, Visualization |
| Version | 0.99.6 |
| 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), matrixStats (>= 0.63.0), 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | quantMSImageR_0.99.6.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | quantMSImageR_0.99.6.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/quantMSImageR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/quantMSImageR |
| Bioc Package Browser | https://code.bioconductor.org/browse/quantMSImageR/ |
| Package Short Url | https://bioconductor.org/packages/quantMSImageR/ |
| Package Downloads Report | Download Stats |