glycoTraitR
This is the released version of glycoTraitR; for the devel version, see glycoTraitR.
Compute and analyze the glycan structrual traits from GPSM data
Bioconductor version: Release (3.23)
GlycoTraitR is an R package for analyzing glycoproteomics data, particularly glycopeptide-spectrum matches (GPSMs). It supports results generated by the pGlyco3 and Glyco-Decipher search engines. The package parses glycan structures, computes monosaccharide compositions and structural traits, and performs differential analysis of glycan heterogeneity. It constructs trait-by-PSM matrices stored in a SummarizedExperiment object, supports user-defined structural motifs, and provides visualization utilities for interpreting glycan trait changes.
Author: Bingyuan Zhang [aut, cre]
, Koichi Himori [aut], Yusuke Matsui [aut, fnd]
Maintainer: Bingyuan Zhang <zhang.bingyuan.w8 at f.mail.nagoya-u.ac.jp>
citation("glycoTraitR")):
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("glycoTraitR")
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("glycoTraitR")| Quick Start | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | MassSpectrometry, Proteomics, Software, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | igraph, SummarizedExperiment, pbapply, car, ggplot2, rlang |
| System Requirements | |
| URL | https://github.com/matsui-lab/glycoTraitR |
| Bug Reports | https://github.com/matsui-lab/glycoTraitR/issues |
See More
| Suggests | knitr, BiocStyle, rmarkdown, markdown, testthat (>= 3.0.0) |
| 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 | glycoTraitR_1.0.0.tar.gz |
| Windows Binary (x86_64) | glycoTraitR_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | glycoTraitR_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | glycoTraitR_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/glycoTraitR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/glycoTraitR |
| Bioc Package Browser | https://code.bioconductor.org/browse/glycoTraitR/ |
| Package Short Url | https://bioconductor.org/packages/glycoTraitR/ |
| Package Downloads Report | Download Stats |