### Install and Run gRodon using Docker

Source: https://github.com/jlw-ecoevo/grodon2/blob/master/README.md

These commands demonstrate how to pull a gRodon Docker image and start an interactive session. Once inside the container, you can launch an R session and use the gRodon package.

```bash
# pull the image 
# shengwei/grodon:latest for gRodon v1.0.0
$ docker pull shengwei/grodon2:latest

# start an interactive container
$ docker run -ti --rm shengwei/grodon2:latest
```

```bash
$ root@5218b31cd695:/mnt# R
```

```r
> library(gRodon)
> library(Biostrings)
> path_to_genome <- system.file('extdata',
  'GCF_000349925.2_ASM34992v2_cds_from_genomic.fna.gz',
  package = 'gRodon')
> genes <- readDNAStringSet(path_to_genome)
> highly_expressed <- grepl("ribosomal protein",names(genes),ignore.case = T)
> predictGrowth(genes, highly_expressed)
```

--------------------------------

### Install gRodon R Package

Source: https://github.com/jlw-ecoevo/grodon2/blob/master/README.md

Install the gRodon R package from GitHub using the devtools package. Ensure you have devtools installed.

```R
devtools::install_github("jlw-ecoevo/gRodon2")
```

--------------------------------

### Predict Microbial Growth Rate with gRodon

Source: https://github.com/jlw-ecoevo/grodon2/blob/master/README.md

This is a minimal example demonstrating how to use the `predictGrowth` function from the gRodon package. It requires loading the gRodon and Biostrings libraries, loading an example genome, identifying highly expressed genes (ribosomal proteins), and then running the prediction.

```r
library(gRodon)
library(Biostrings)

# Load in example genome (Streptococcus pyogenes M1, downloaded from RefSeq) 
# included with gRodon
path_to_genome <- system.file('extdata',
  'GCF_000349925.2_ASM34992v2_cds_from_genomic.fna.gz',
  package = 'gRodon')
genes <- readDNAStringSet(path_to_genome)

# Search pre-existing annotations for ribosomal proteins, which we
# will use as our set of highly expressed genes
highly_expressed <- grepl("ribosomal protein",names(genes),ignore.case = T)

# Run the gRodon growth prediction pipeline
predictGrowth(genes, highly_expressed)
```

--------------------------------

### Install gRodon Dependencies

Source: https://github.com/jlw-ecoevo/grodon2/blob/master/README.md

Install necessary Bioconductor and CRAN packages for gRodon. This includes Biostrings, coRdon, and matrixStats.

```R
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biostrings")
BiocManager::install("coRdon")
install.packages("matrixStats")
```

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