glysmith

One Ring to rule them all. — The Lord of the Rings

Be overwhelmed by the complexity of glycoverse?

Imagine a package, performing all analysis you need, PCA, DEA, enrichment, or even advanced glycan derived trait analysis, in just one line of code.

Try glysmith! Perform the comprehensive analysis pipeline with one function call.

output_short.mp4

Installation

You can install the latest release of glysmith from r-universe (recommended):

# install.packages("pak")
pak::repo_add(glycoverse = "https://glycoverse.r-universe.dev")
pak::pkg_install("glysmith")

Or from GitHub:

pak::pkg_install("glycoverse/glysmith@*release")

Or install the development version (NOT recommended):

pak::pkg_install("glycoverse/glysmith")

glysmith is a high-level package, depending on quite a lot mature packages. After installing glysmith, you also need to install additional dependencies to use this package:

glysmith::check_glysmith_deps()

Example

library(glyread)
library(glysmith)

exp <- read_pglyco3("pglyco3_result.txt", sample_info = "sample_info.csv")

# One line of code for the comprehensive analysis pipeline
result <- forge_analysis(exp)

# One line of code to save the results
quench_result(result, "path/to/save")

# One line of code to generate a report
polish_report(result, "report.html")

After running the above quench_result line, you will get an organized result folder:

And after running the above polish_report line, you will get a report in HTML format and automatically open it in your default browser:

Note: Here we set use_ai to TRUE to enable LLM-assisted report generation.