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AlphaGenomeR is currently available from GitHub and is pending release on Bioconductor. Installation requires two steps: the R package itself and the alphagenome Python package that handles gRPC communication with the API.
Before you install, make sure you have all three prerequisites:
  • Python >= 3.10 — required by reticulate to load the AlphaGenome Python SDK
  • alphagenome Python package — install with pip install alphagenome
  • AlphaGenome API key — obtain a free, non-commercial key from the AlphaGenome Science Page

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Install from GitHub

1

Install the R package

Install AlphaGenomeR directly from the BDB-Genomics GitHub repository using devtools:
# install.packages("devtools")
devtools::install_github("BDB-Genomics/AlphaGenomeR")
This installs AlphaGenomeR and its R dependencies (reticulate, glue, methods).
2

Install the Python dependency

AlphaGenomeR uses reticulate to call the official AlphaGenome Python SDK. Install it with pip:
pip install alphagenome
If you use conda or a virtual environment, activate it first so reticulate discovers the correct Python installation.
3

Get your API key

AlphaGenome requires a free, non-commercial API key for all prediction requests. Obtain yours from the AlphaGenome Science Page.Store your key securely — never hard-code it in scripts you share or commit to version control. A common pattern is to use an environment variable:
# In your .Renviron file:
# ALPHAGENOME_API_KEY=your_key_here

api_key <- Sys.getenv("ALPHAGENOME_API_KEY")

​
Install from Bioconductor (upcoming)

AlphaGenomeR is pending submission to Bioconductor. Once accepted, you will be able to install it with BiocManager: 
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("AlphaGenomeR")
Check the Bioconductor package page for availability status.

​
Verify installation

After installing, load the package and confirm that the alphagenome Python module is accessible: 
library(AlphaGenomeR)

# Check that the alphagenome Python module is available
reticulate::py_module_available("alphagenome")
#> [1] TRUE
If the check returns FALSE, reticulate cannot find the Python installation where you ran pip install alphagenome. See the troubleshooting section below.

​
Troubleshooting

reticulate may be pointing to a different Python installation than the one where you installed alphagenome. Check which Python reticulate is using:
reticulate::py_config()
To point reticulate at a specific Python binary or virtual environment, set the path before loading the package:
reticulate::use_python("/path/to/python3")
# or for a virtual environment:
reticulate::use_virtualenv("/path/to/venv")
You must call use_python() or use_virtualenv() before any other reticulate call in a fresh R session.
If reticulate::py_module_available("alphagenome") returns FALSE, install the package into the Python environment that reticulate is using:
pip install alphagenome
Confirm the package version meets the minimum requirement (>= 0.6.1):
pip show alphagenome
If you are using a conda environment, use conda install or pip inside the activated environment.
If alphagenome_query() returns an authentication error, verify that your key is valid and being passed correctly:
# Check that the variable is not empty
api_key <- Sys.getenv("ALPHAGENOME_API_KEY")
nchar(api_key) > 0
#> [1] TRUE
API keys are restricted to non-commercial research use. Ensure your usage complies with the AlphaGenome terms of service.
If devtools::install_github() fails, make sure devtools is installed and that you have a working internet connection:
install.packages("devtools")
devtools::install_github("BDB-Genomics/AlphaGenomeR")
On Linux, you may need system build tools (build-essential, libcurl4-openssl-dev, libssl-dev). On macOS, install Xcode Command Line Tools with xcode-select --install.

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