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glycoverse

The ‘glycoverse’ is a set of packages that together form a comprehensive pipeline for glycomics and glycoproteomics data analysis. This package is designed to make it easy to install and load multiple ‘glycoverse’ packages in a single step.

Installation

You can install the latest release of glycoverse from GitHub with:

# install.packages("remotes")
remotes::install_github("glycoverse/glycoverse@*release")

Or install the development version:

remotes::install_github("glycoverse/glycoverse")

Documentation

We have two case studies that showcase the basic workflow of glycoverse:

Choose one of them to get started, and then refer to the documentation of the individual packages for more details.

Usage

library(glycoverse) will load all the core packages in the glycoverse ecosystem:

This includes:

Omics data analysis

Glycan structure analysis

  • glyrepr, for glycan structure representation
  • glyparse, for glycan structure parsing
  • glymotif, for glycan structure motif analysis
  • glydet, for glycan derived trait analysis
  • glyenzy, for glycan biosynthesis pathway analysis

You also get a condensed summary of conflicts with other packages you have loaded:

library(glycoverse)
#> ── Attaching core glycoverse packages ───────────────── glycoverse 0.0.0.9000 ──
#> ✔ glyclean 0.6.4     ✔ glyparse 0.4.4
#> ✔ glydet   0.3.0     ✔ glyread  0.6.1
#> ✔ glyenzy  0.2.2     ✔ glyrepr  0.7.3
#> ✔ glyexp   0.9.1     ✔ glystats 0.4.2
#> ✔ glymotif 0.8.0     ✔ glyvis   0.1.2
#> ── Conflicts ───────────────────────────────────────── glycoverse_conflicts() ──
#> ✖ glyclean::aggregate() masks stats::aggregate()
#> ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

And you can update all the packages with glycoverse_update():

glycoverse_update()
#> All glycoverse packages up-to-date