Documentation & Vignettes
Everything you need to script GCModeller lives in the R# vignettes: the function reference for every software module, with parameters, defaults and runnable examples. Start from the vignettes index — it is the front door to the whole API.
R# Vignettes Index
The official reference documentation for GCModeller scripting. Each module of the framework — genome annotation, virtual-cell modeling, virtual perturbation experiments, pan-omics analysis — ships its own set of vignette pages documenting every exported R# function.
gcmodeller.org/vignettes/index.html ↗How to find a function
Open the index
Go to gcmodeller.org/vignettes/index.html. The landing page lists every documented module of the framework.
Pick your module
Navigate to the module that matches your task — annotation, FBA, network inference, omics statistics, and so on.
Read the function page
Every exported R# function is documented with its parameters, types, default values and a runnable usage example you can adapt.
Searching tips
# find any vignette page mentioning a function name,
# directly from your favourite search engine:
site:gcmodeller.org/vignettes "limma"
site:gcmodeller.org/vignettes "gsea"
site:gcmodeller.org/vignettes "flux balance"Vignette pages are plain, indexable HTML — a targeted search for the function name you remember from a paper or a forum thread will usually land you on the exact reference page.
Related resources
Source & Issues
Browse the implementation of any algorithm, file a bug report or request a feature on GitHub.
github.com/SMRUCC/GCModeller ↗Container Image
Tagged releases of the Ubuntu environment image in which GCModeller and its R# runtime run.
hub.docker.com · gcmodeller-env ↗bio.tools Entry
The registry entry describing GCModeller's operations and tool types for the bioinformatics community.
bio.tools/gcmodeller ↗