specL
This is the development version of specL; for the stable release version, see specL.
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Bioconductor version: Development (3.24)
provides a functions for generating spectra libraries that can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software. The package is developed, tested and used at the Functional Genomics Center Zurich
Author: Christian Panse [aut, cre]
, Jonas Grossmann [aut]
, Christian Trachsel [aut], Witold E. Wolski [ctb]
Maintainer: Christian Panse <cp at fgcz.ethz.ch>
citation("specL")):
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("specL")
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("specL")| Automatic specL Workflow | HTML | R Script |
| Introduction to specL | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | MassSpectrometry, Proteomics, Software |
| Version | 1.47.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 years) |
| License | GPL-3 |
| Depends | R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3) |
| Imports | |
| System Requirements | |
| URL | http://bioconductor.org/packages/specL/ |
| Bug Reports | https://github.com/fgcz/specL/issues |
See More
| Suggests | BiocGenerics, BiocStyle(>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | msqc1, NestLink |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | specL_1.47.0.tar.gz |
| Windows Binary (x86_64) | specL_1.47.0.zip |
| macOS Binary (big-sur-x86_64) | specL_1.47.0.tgz |
| macOS Binary (sonoma-arm64) | specL_1.47.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/specL |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/specL |
| Bioc Package Browser | https://code.bioconductor.org/browse/specL/ |
| Package Short Url | https://bioconductor.org/packages/specL/ |
| Package Downloads Report | Download Stats |