TargetSearch
This is the released version of TargetSearch; for the devel version, see TargetSearch.
A package for the analysis of GC-MS metabolite profiling data
Bioconductor version: Release (3.23)
This packages provides a flexible, fast and accurate method for targeted pre-processing of GC-MS data. The user provides a (often very large) set of GC chromatograms and a metabolite library of targets. The package will automatically search those targets in the chromatograms resulting in a data matrix that can be used for further data analysis.
Author: Alvaro Cuadros-Inostroza [aut, cre], Jan Lisec [aut], Henning Redestig [aut], Matt Hannah [aut]
Maintainer: Alvaro Cuadros-Inostroza <acuadros+bioc at gmail.com>
citation("TargetSearch")):
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")
BiocManager::install("TargetSearch")
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("TargetSearch")| RI correction extra | R Script | |
| The TargetSearch Package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DecisionTree, ImmunoOncology, MassSpectrometry, Preprocessing, Software |
| Version | 2.14.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (17.5 years) |
| License | GPL (>= 2) |
| Depends | |
| Imports | graphics, grDevices, methods, ncdf4, stats, utils, assertthat |
| System Requirements | |
| URL | https://github.com/acinostroza/TargetSearch |
| Bug Reports | https://github.com/acinostroza/TargetSearch/issues |
See More
| Suggests | TargetSearchData, BiocStyle, knitr, tinytest |
| 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 | TargetSearch_2.14.0.tar.gz |
| Windows Binary (x86_64) | TargetSearch_2.14.0.zip |
| macOS Binary (big-sur-x86_64) | TargetSearch_2.14.0.tgz |
| macOS Binary (sonoma-arm64) | TargetSearch_2.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TargetSearch |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TargetSearch |
| Bioc Package Browser | https://code.bioconductor.org/browse/TargetSearch/ |
| Package Short Url | https://bioconductor.org/packages/TargetSearch/ |
| Package Downloads Report | Download Stats |