The goal of glyread is to read and process quantification results from
common glycomics and glycoproteomics software, such as Byonic, StrucGP,
or pGlyco, and convert them into a glyexp::expriment() object (from
the glyexp package) for further
analysis.
You can install the latest release of glyread from r-universe (recommended):
# install.packages("pak")
pak::repo_add(glycoverse = "https://glycoverse.r-universe.dev")
pak::pkg_install("glyread")Or from GitHub:
pak::pkg_install("glycoverse/glyread@*release")Or install the development version (NOT recommended):
pak::pkg_install("glycoverse/glyread")glyread is the entry point for the glycoverse ecosystem. It provides
a unified interface for reading and processing data from various
glycomics and glycoproteomics software, and converting them into a
glyexp::experiment() object for further analysis.
Used pGlyco3 and pGlycoQuant for glycopeptide identification and
quantification? Try read_pglyco3_pglycoquant()!
library(glyread)
exp <- read_pglyco3_pglycoquant(
"path/to/pGlyco3-pGlycoQuant/result/Quant.spectra.list",
sample_info = "path/to/sample_info.csv",
quant_method = "label-free",
glycan_type = "N"
)