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")Important Note
glycoverse before v0.1.1 had serious bugs in dependency management. We recommend all users to update to the latest version of glycoverse, and call glycoverse::glycoverse_update() to update all the packages in the glycoverse ecosystem.
Besides, we are progressively uploading glycoverse packages to CRAN. Every time a package is shifted to CRAN, we will update the glycoverse meta-package to depend on the CRAN version of that package. So come back from time to time to check if you have the latest version of 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:
library(glycoverse)
#> ── Attaching core glycoverse packages ───────────────── glycoverse 0.1.3.9000 ──
#> ✔ glyclean 0.9.1 ✔ glyparse 0.5.3
#> ✔ glydet 0.6.5 ✔ glyread 0.8.2
#> ✔ glydraw 0.0.0.9000 ✔ glyrepr 0.9.0
#> ✔ glyexp 0.10.4 ✔ glystats 0.5.5
#> ✔ glymotif 0.11.2 ✔ glyvis 0.4.1
#> ── Conflicts ───────────────────────────────────────── glycoverse_conflicts() ──
#> ✖ glyclean::aggregate() masks stats::aggregate()
#> ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorsThis includes:
Omics data analysis
- glyexp, for data management
- glyread, for data import
- glyclean, for data cleaning and preprocessing
- glystats, for statistical analysis
- glyvis, for data visualization
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
- glydraw, for glycan structure visualization
You can also install the non-core glycoverse packages if needed:
- glyenzy, for glycan biosynthesis pathway analysis
- glydb, for glycan database
- glyanno, for glycan annotation
- glysmith, for full analytical pipeline
You can get a situation report of all the packages in the glycoverse ecosystem with glycoverse_sitrep():
glycoverse_sitrep()
#> ── R & RStudio ─────────────────────────────────────────────────────────────────
#> • R: 4.5.1
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#> CRAN: https://cloud.r-project.org
#> ── Core packages ───────────────────────────────────────────────────────────────
#> • glyexp (0.10.4)
#> • glyread (0.8.2)
#> • glyclean (0.9.1)
#> • glystats (0.5.5)
#> • glyvis (0.4.1)
#> • glyrepr (0.9.0)
#> • glyparse (0.5.3)
#> • glymotif (0.11.2)
#> • glydet (0.6.5)
#> • glydraw (0.0.0.9000)
#> ── Non-core packages ───────────────────────────────────────────────────────────
#> • glyenzy (0.4.1)
#> • glydb (0.3.1)
#> • glyanno (0.1.0)
#> • glysmith (0.0.0 < 0.0.0.9000)To list all dependencies of glycoverse core packages, run:
glycoverse_deps(recursive = TRUE) # recursive = TRUE to list dependencies of each package
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#> CRAN: https://cloud.r-project.org
#> # A tibble: 118 × 6
#> package source remote upstream local behind
#> <chr> <chr> <chr> <chr> <chr> <lgl>
#> 1 ade4 cran <NA> 1.7-23 1.7.23 FALSE
#> 2 AnnotationDbi bioconductor <NA> 1.72.0 1.72.0 FALSE
#> 3 askpass cran <NA> 1.2.1 1.2.1 FALSE
#> 4 backports cran <NA> 1.5.0 1.5.0 FALSE
#> 5 Biobase bioconductor <NA> 2.70.0 2.70.0 FALSE
#> 6 BiocGenerics bioconductor <NA> 0.56.0 0.56.0 FALSE
#> 7 Biostrings bioconductor <NA> 2.78.0 2.78.0 FALSE
#> 8 bit cran <NA> 4.6.0 4.6.0 FALSE
#> 9 bit64 cran <NA> 4.6.0-1 4.6.0.1 FALSE
#> 10 blob cran <NA> 1.2.4 1.2.4 FALSE
#> # ℹ 108 more rowsAnd you can update all the packages with glycoverse_update():