bbglab/oncodrive3d repository overview

⁠Oncodrive3D

Oncodrive3D is a fast and accurate computational method designed to analyze patterns of somatic mutation across tumors, with the goal of identifying three-dimensional (3D) clusters of missense mutations and detecting genes under positive selection.

The method leverages AlphaFold 2-predicted protein structures and Predicted Aligned Error (PAE) to define residue contacts within the protein's 3D space. When available, it integrates mutational profiles to build an accurate background model of neutral mutagenesis. By applying a novel rank-based statistical approach, Oncodrive3D scores potential 3D clusters and computes empirical p-values.

⁠Container Images

Oncodrive3D ships three image variants, each layered on top of the previous so you can pick the smallest one that covers your workflow:

⁠Docker

docker pull bbglab/oncodrive3d:latest
docker run --rm -v "$PWD":/data bbglab/oncodrive3d:latest \
    oncodrive3d run -i /data/<input_maf> -p /data/<mut_profile> \
                    -d /data/<build_folder> -C <cohort_name> -o /data/<output_dir>

⁠Singularity

singularity pull oncodrive3d.sif docker://bbglab/oncodrive3d:latest
singularity exec oncodrive3d.sif oncodrive3d run \
    -i <input_maf> -p <mut_profile> -d <build_folder> -C <cohort_name>

⁠Testing

To verify that Oncodrive3D is installed and configured correctly, you can perform a test run using the provided test input files:

oncodrive3d run -d <build_folder> \
                -i ./test/input/maf/TCGA_WXS_ACC.in.maf \
                -p ./test/input/mut_profile/TCGA_WXS_ACC.sig.json \
                -o ./test/output/ -C TCGA_WXS_ACC

Check the output in the test/output/ directory to ensure the analysis completes successfully.

⁠Building Annotations & Plotting

Oncodrive3D ships with an optional plotting pipeline: run oncodrive3d build-annotations once to cache structural/functional tracks, then use oncodrive3d plot and/or chimerax-plot to generate plots and tables that help interpret the clustering signal and distinguish real biology from artifacts.

See the Annotation & plotting workflow⁠ for prerequisites, usage examples, and output descriptions.

⁠Parallel Processing on Multiple Cohorts

Oncodrive3D ships with a Nextflow⁠ pipeline for running multiple cohorts in parallel. See the Oncodrive3D Pipeline documentation⁠ for setup, input layout, and options.

⁠License

Oncodrive3D is available to the general public subject to certain conditions described in its LICENSE⁠.

⁠Credits

Oncodrive3D was originally written by Stefano Pellegrini.

We thank the following people for their assistance in the development of this tool:

• @koszulordie⁠
• @FedericaBrando⁠
• @FerriolCalvet⁠
• @odove⁠

⁠Citation

If you use Oncodrive3D in your research, please cite: