ptairMS
This is the released version of ptairMS; for the devel version, see ptairMS.
Pre-processing PTR-TOF-MS Data
Bioconductor version: Release (3.23)
This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a singl
Author: camille Roquencourt [aut, cre]
Maintainer: camille Roquencourt <camille.roquencourt at hotmail.fr>
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.citation("ptairMS")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ptairMS")
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("ptairMS")| ptaiMS: Processing and analysis of PTR-TOF-MS data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, MassSpectrometry, Metabolomics, PeakDetection, Preprocessing, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | |
| Imports | Biobase, bit64, chron, data.table, doParallel, DT, enviPat, foreach, ggplot2, graphics, grDevices, ggpubr, gridExtra, Hmisc, methods, minpack.lm, MSnbase, parallel, plotly, rhdf5, rlang, Rcpp, shiny, shinyscreenshot, signal, scales, stats, utils |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/camilleroquencourt/ptairMS/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData, ropls |
| Linking To | Rcpp |
| 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 | ptairMS_1.20.0.tar.gz |
| Windows Binary (x86_64) | ptairMS_1.20.0.zip |
| macOS Binary (big-sur-x86_64) | ptairMS_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | ptairMS_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ptairMS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ptairMS |
| Bioc Package Browser | https://code.bioconductor.org/browse/ptairMS/ |
| Package Short Url | https://bioconductor.org/packages/ptairMS/ |
| Package Downloads Report | Download Stats |