AlphaGenomeR

An R interface to Google DeepMind's AlphaGenome API.

Overview

AlphaGenomeR provides a small set of wrapper functions for querying AlphaGenome and extracting common output modalities in R.

Installation

Development version

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}

BiocManager::install("BDB-Genomics/AlphaGenomeR")

Bioconductor release

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}

BiocManager::install("AlphaGenomeR")

Requirements

• R >= 4.0
• Python >= 3.10
• alphagenome Python package
• valid AlphaGenome API key
• internet access for live API queries

Setup

AlphaGenomeR uses reticulate to call the Python client. Point reticulate to the Python environment that has alphagenome installed before loading the package:

Sys.setenv(
  RETICULATE_PYTHON = "/path/to/miniconda3/envs/alphagenomer/bin/python"
)

library(AlphaGenomeR)

Quick Start

results <- alphagenome_query(
  api_key = "YOUR_API_KEY",
  genomic_region = "chr17:42560601-43560601",
  ontology_terms = "UBERON:0002048",
  requested_outputs = c("RNA_SEQ", "ATAC")
)

rna <- alphagenome_get_rna_seq(results)
atac <- alphagenome_get_atac(results)

Output Structure

alphagenome_query() returns a named list of modality results.

Each extractor returns one modality as a list with:

• values - numeric matrix or array of predictions
• metadata - data frame describing each track

Supported Outputs

• alphagenome_get_rna_seq()
• alphagenome_get_atac()
• alphagenome_get_cage()
• alphagenome_get_dnase()
• alphagenome_get_chip_tf()
• alphagenome_get_chip_histone()
• alphagenome_get_splice_sites()
• alphagenome_get_splice_junctions()
• alphagenome_get_splice_usage()
• alphagenome_get_procap()
• alphagenome_get_contact_maps()

Development

Run checks locally before submitting changes:

devtools::test()
devtools::check()

The GitHub Actions workflow runs the same checks in CI.

Citation

If you use AlphaGenomeR, please cite the package:

citation("AlphaGenomeR")

License

Apache License 2.0