CrcBiomeScreen

An R package for colorectal cancer screening and microbiome analysis.

Installation

Option 1 — Install directly from GitHub

You can install CrcBiomeScreen directly in R:

install.packages("remotes")
remotes::install_github("omicsForestry/CrcBiomeScreen", force = TRUE)

Option 2 — Use the provided conda environment

This will set up all system and R dependencies. After activating the environment, you still need to install the package itself from GitHub.

# Create and activate environment
conda env create -f environment.yml
conda activate CrcBiomeScreen

Then, inside R:

install.packages("remotes")
remotes::install_github("omicsForestry/CrcBiomeScreen", force = TRUE)

Usage

library(CrcBiomeScreen)

Run Vignette

# Install BiocStyle for vignette rendering
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BiocStyle")
library(BiocStyle)
remotes::install_github("omicsForestry/CrcBiomeScreen", build_vignettes = TRUE, force = TRUE)
vignette("CrcBiomeScreen")

Package Structure

• R/: Core functions
• data/: Example datasets
• vignettes/: Usage examples
• tests/: Testing functions
• man/ : Documentation files

Roadmap

• CompareModels()
• SelectImportanceFeatures()
• SHAP values analysis

This package is licensed under the MIT License.