ncGTW
This is the released version of ncGTW; for the devel version, see ncGTW.
Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection
Bioconductor version: Release (3.23)
The purpose of ncGTW is to help XCMS for LC-MS data alignment. Currently, ncGTW can detect the misaligned feature groups by XCMS, and the user can choose to realign these feature groups by ncGTW or not.
Author: Chiung-Ting Wu <ctwu at vt.edu>
Maintainer: Chiung-Ting Wu <ctwu at vt.edu>
citation("ncGTW")):
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("ncGTW")
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("ncGTW")| ncGTW User Manual | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, MassSpectrometry, Metabolomics, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | GPL-2 |
| Depends | methods, BiocParallel, xcms |
| Imports | Rcpp, grDevices, graphics, stats |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/ChiungTingWu/ncGTW/issues |
See More
| Suggests | BiocStyle, knitr, testthat, rmarkdown |
| 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 | ncGTW_1.26.0.tar.gz |
| Windows Binary (x86_64) | ncGTW_1.26.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | ncGTW_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | ncGTW_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ncGTW |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ncGTW |
| Bioc Package Browser | https://code.bioconductor.org/browse/ncGTW/ |
| Package Short Url | https://bioconductor.org/packages/ncGTW/ |
| Package Downloads Report | Download Stats |