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")):
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_0.99.2.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | glycoTraitR_0.99.2.tgz |
| macOS Binary (big-sur-arm64) | |
| 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 |