# 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:
```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.
```bash
# Create and activate environment
conda env create -f environment.yml
conda activate CrcBiomeScreen
```
Then, inside R:
```R
install.packages("remotes")
remotes::install_github("omicsForestry/CrcBiomeScreen", force = TRUE)
```
## Usage
```r
library(CrcBiomeScreen)
```
### Run Vignette
```r
# 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](LICENSE.md).
