MassSpecWavelet
This is the development version of MassSpecWavelet; for the stable release version, see MassSpecWavelet.
Peak Detection for Mass Spectrometry data using wavelet-based algorithms
Bioconductor version: Development (3.24)
Peak Detection in Mass Spectrometry data is one of the important preprocessing steps. The performance of peak detection affects subsequent processes, including protein identification, profile alignment and biomarker identification. Using Continuous Wavelet Transform (CWT), this package provides a reliable algorithm for peak detection that does not require any type of smoothing or previous baseline correction method, providing more consistent results for different spectra. See
Author: Pan Du [aut], Warren Kibbe [aut], Simon Lin [aut], Sergio Oller Moreno [aut, cre]
Maintainer: Sergio Oller Moreno <sergioller at gmail.com>
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("MassSpecWavelet")):
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("MassSpecWavelet")
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("MassSpecWavelet")| Finding local maxima | HTML | R Script |
| Using the MassSpecWavelet package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, PeakDetection, Proteomics, Software |
| Version | 1.79.2 |
| In Bioconductor since | BioC 2.0 (R-2.5) (19.5 years) |
| License | LGPL (>= 2) |
| Depends | |
| Imports | |
| System Requirements | |
| URL | https://github.com/zeehio/MassSpecWavelet |
| Bug Reports | http://github.com/zeehio/MassSpecWavelet/issues |
See More
| Suggests | signal, waveslim, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), bench |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | cosmiq, xcms, NMRphasing, Rnmr1D, speaq |
| Suggests Me | downlit, metabodecon |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MassSpecWavelet_1.79.2.tar.gz |
| Windows Binary (x86_64) | MassSpecWavelet_1.79.2.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | MassSpecWavelet_1.79.2.tgz |
| macOS Binary (sonoma-arm64) | MassSpecWavelet_1.79.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MassSpecWavelet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MassSpecWavelet |
| Bioc Package Browser | https://code.bioconductor.org/browse/MassSpecWavelet/ |
| Package Short Url | https://bioconductor.org/packages/MassSpecWavelet/ |
| Package Downloads Report | Download Stats |