Oncodrive3D 1.0.8__tar.gz → 1.0.9__tar.gz

oncodrive3d-1.0.9/.dockerignore

@@ -0,0 +1 @@
+.env

{oncodrive3d-1.0.8 → oncodrive3d-1.0.9}/.gitignore

@@ -192,4 +192,7 @@ run_*
 
 # VSC
 launch.json
-.vscode
+.vscode
+
+# Docker build artifacts (ChimeraX installer staged into context)
+chimerax*.deb

oncodrive3d-1.0.9/Dockerfile

@@ -0,0 +1,106 @@
+# Multi-target Dockerfile for Oncodrive3D.
+#
+# Targets (each builds on the previous; pick with `--target`):
+#   light    (default)  - oncodrive3d only.
+#                         Covers `run` and `plot` (including normal-tissue
+#                         mutability runs). No external prerequisites to build.
+#   chimerax            - light + ChimeraX. Adds `chimerax-plot`. Requires the
+#                         ChimeraX installer staged in the build context as
+#                         `chimerax.deb` (override via --build-arg CHIMERAX_DEB=).
+#   full                - chimerax + bgdata caches (hg38, mm39) + PDB_Tool.
+#                         Adds `build-datasets` and `build-annotations`.
+#
+# Examples:
+#   docker build --target light    -t oncodrive3d:1.0.9         -t oncodrive3d:latest   .
+#   docker build --target chimerax -t oncodrive3d:1.0.9-chimerax -t oncodrive3d:chimerax .
+#   docker build --target full     -t oncodrive3d:1.0.9-full     -t oncodrive3d:full     .
+
+# Stage 1: build the oncodrive3d wheel
+FROM ghcr.io/astral-sh/uv:0.5-python3.10-bookworm AS build-stage
+
+ENV UV_COMPILE_BYTECODE=1
+
+WORKDIR /oncodrive3d
+
+COPY uv.lock uv.lock
+COPY pyproject.toml pyproject.toml
+COPY scripts scripts
+COPY README.md README.md
+
+RUN mkdir -p /root/.cache/uv \
+    && uv sync --frozen --no-dev \
+    && uv build
+
+# Stage 2: compile PDB_Tool from source (only consumed by the `full` target)
+FROM python:3.10-bullseye AS pdb-tool-stage
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        build-essential ca-certificates git \
+    && git clone --depth 1 https://github.com/realbigws/PDB_Tool.git /pdb-tool \
+    && make -C /pdb-tool/source_code \
+    && rm -rf /var/lib/apt/lists/*
+
+# Stage 3 (target=light): just oncodrive3d. No ChimeraX, no PDB_Tool, no bgdata.
+# Debian 11 base keeps layers shareable with the downstream targets that need
+# libssl1.1 + libffi7 for the Ubuntu 20.04 ChimeraX .deb.
+FROM python:3.10-bullseye AS light
+
+COPY --from=build-stage /oncodrive3d/dist /oncodrive3d/dist
+WORKDIR /oncodrive3d
+RUN pip install --no-cache-dir dist/*.tar.gz
+
+LABEL Author="stefano.pellegrini@irbbarcelona.org"
+
+CMD ["oncodrive3D"]
+
+# Stage 4 (target=chimerax): light + ChimeraX
+FROM light AS chimerax
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+ARG CHIMERAX_DEB=chimerax.deb
+COPY ${CHIMERAX_DEB} /tmp/chimerax.deb
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends /tmp/chimerax.deb \
+    && rm /tmp/chimerax.deb \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Stage 5 (target=full): chimerax + bgdata caches (hg38, mm39) + PDB_Tool
+FROM chimerax AS full
+
+ENV BGDATA_LOCAL="/bgdatacache" \
+    BBGLAB_HOME="/home/user/.config/bbglab/"
+
+# PDB_Tool binary (for `build-annotations`)
+COPY --from=pdb-tool-stage /pdb-tool/PDB_Tool /usr/local/bin/PDB_Tool
+
+RUN install -d -m 0755 "$BGDATA_LOCAL" "$BBGLAB_HOME"
+
+# Write bgdata configuration
+RUN echo "# Version of the bgdata config file\n\
+version = 2\n\
+\n\
+# The default local folder to store the data packages\n\
+local_repository = \"$BGDATA_LOCAL\"\n\
+\n\
+# The remote URL to download the data packages\n\
+remote_repository = \"https://bbglab.irbbarcelona.org/bgdata\"\n\
+\n\
+# If you want to force bgdata to work only locally\n\
+# offline = True\n\
+\n\
+# Cache repositories\n\
+[cache_repositories]" > "$BBGLAB_HOME/bgdatav2.conf"
+
+# Pre-fetch and prepare genome data (needed by `build-datasets`)
+RUN apt-get update && apt-get install -y --no-install-recommends curl \
+    && pip install --no-cache-dir bgdata bgreference \
+    && bgdata get datasets/genomereference/hg38 \
+    && bgdata get datasets/genomereference/mm39 \
+    && python3 -c "from bgreference import hg38; hg38(1, 1300000, 3000)" \
+    && python3 -c "from bgreference import mm39; mm39(1, 1300000, 3000)" \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN chmod -R 0755 "$BGDATA_LOCAL"

oncodrive3d-1.0.9/PKG-INFO

@@ -0,0 +1,262 @@
+Metadata-Version: 2.4
+Name: Oncodrive3D
+Version: 1.0.9
+Summary: Oncodrive3D is a method designed to analyse patterns of somatic mutations across tumors to identify three-dimensional (3D) clusters of missense mutations and detect genes that are under positive selection.
+Project-URL: Homepage, https://github.com/bbglab/clustering_3d
+Project-URL: Repository, https://github.com/bbglab/clustering_3d
+Project-URL: Issues, https://github.com/bbglab/clustering_3d/issues
+Author-email: "BBGLab (Barcelona Biomedical Genomics Lab)" <bbglab@irbbarcelona.org>, Stefano Pellegrini <stefano.pellegrini@irbbarcelona.org>
+License: GNU Affero General Public License v3 or later (AGPLv3+)
+License-File: LICENSE
+Keywords: bbglab,bioinformatics,driversprediction,positiveselection
+Requires-Python: >=3.10
+Requires-Dist: adjusttext==1.1.1
+Requires-Dist: aiohttp>=3.11.10
+Requires-Dist: bgreference==0.7
+Requires-Dist: bio==1.7.1
+Requires-Dist: colorcet==3.0.1
+Requires-Dist: daiquiri>=3.3.0
+Requires-Dist: matplotlib>=3.6.2
+Requires-Dist: networkx==2.7.1
+Requires-Dist: numpy==1.26.4
+Requires-Dist: pandas==1.4.2
+Requires-Dist: progressbar2==4.0.0
+Requires-Dist: pypdl==1.4.5
+Requires-Dist: pytabix==0.0.2
+Requires-Dist: scikit-learn>=1.3.0
+Requires-Dist: scipy>=1.7.3
+Requires-Dist: seaborn>=0.12.2
+Requires-Dist: setuptools==61.2.0
+Requires-Dist: statsmodels>=0.13.2
+Requires-Dist: tqdm>=4.67.1
+Provides-Extra: linting
+Requires-Dist: ruff>=0.8.3; extra == 'linting'
+Description-Content-Type: text/markdown
+
+# 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.
+
+[![License: AGPL v3](https://img.shields.io/badge/License-AGPL_v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)
+[![docker](https://img.shields.io/docker/v/bbglab/oncodrive3d?logo=docker)](https://hub.docker.com/r/bbglab/oncodrive3d)
+[![PyPI - Version](https://img.shields.io/pypi/v/oncodrive3d?logo=pypi)](https://pypi.org/project/Oncodrive3D/)
+
+![Graphical abstract of Oncodrive3D](docs/images/graphical_abstract.png "Oncodrive3D")
+
+## Requirements
+
+Python 3.10+ is required. Some systems also need a C/C++ toolchain:
+
+- With sudo privileges:
+
+   ```bash
+   sudo apt install build-essential
+   ```
+
+- On HPC clusters, [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) (or [Mamba](https://mamba.readthedocs.io/en/latest/)) is recommended:
+
+   ```bash
+   conda create -n o3d python=3.10.0
+   conda activate o3d
+   conda install -c conda-forge gxx gcc libxcrypt clang zlib
+   ```
+
+## Installation
+
+- Install via PyPI:
+
+   ```bash
+   pip install oncodrive3d
+   ```
+
+- Alternatively, you can obtain the latest code from the repository and install it for development with pip:
+
+   ```bash
+   git clone https://github.com/bbglab/oncodrive3d.git
+   cd oncodrive3d
+   pip install -e .
+   oncodrive3d --help
+   ```
+
+- Or you can use a modern build tool like [uv](https://github.com/astral-sh/uv):
+
+   ```bash
+   git clone https://github.com/bbglab/oncodrive3d.git
+   cd oncodrive3d
+   uv run oncodrive3d --help
+   ```
+
+## Building Datasets
+
+This step builds the datasets necessary for Oncodrive3D to run the 3D clustering analysis. It is required once after installation or whenever you need to generate datasets for a different organism or apply a specific threshold to define amino acid contacts.
+
+> [!WARNING]
+> This step is time- and resource-intensive: it downloads and processes large amounts of structural data. Ensure adequate disk space, CPU, and a reliable internet connection (AlphaFold, Ensembl, Pfam, and other resources are fetched on demand).
+
+<!-- -->
+
+> [!WARNING]
+> MANE builds force AlphaFold DB v4 structures (non-MANE builds default to v6). PAE files for v4 are no longer hosted after 2025, so MANE builds without `--custom_pae_dir` fall back to binary contact maps. To keep PAE-weighted probability maps, supply precomputed v4 PAE files via `--custom_pae_dir`.
+
+<!-- -->
+
+> [!NOTE]
+> The first time that you run Oncodrive3D building dataset step with a given reference genome, it will download it from our servers. By default the downloaded datasets go to `~/.bgdata`. If you want to move these datasets to another folder you have to define the system environment variable `BGDATA_LOCAL` with an export command.
+
+```text
+Usage: oncodrive3d build-datasets [OPTIONS]
+
+Examples:
+  Basic build (human):
+    oncodrive3d build-datasets -o <build_folder>
+
+  Build with MANE Select transcripts:
+    oncodrive3d build-datasets -o <build_folder> --mane
+
+  Build mouse datasets:
+    oncodrive3d build-datasets -o <build_folder> -s mouse
+```
+
+See `oncodrive3d build-datasets --help` for all options.
+
+For more information on the output of this step, please refer to the [Building Datasets Output Documentation](docs/build_output.md).
+
+> [!TIP]
+> To extend MANE Select structural coverage beyond the AlphaFold MANE bundle, see the [MANE Preprocessing Toolkit](tools/preprocessing/README.md).
+
+## Running 3D Clustering Analysis
+
+See the [Input and Output Documentation](docs/run_input_output.md) for details on inputs and outputs.
+
+### Input
+
+- **Mutations file** (`required`): It can be either:
+  - **<input_maf>**: A Mutation Annotation Format (MAF) file annotated with consequences (e.g., by using [Ensembl Variant Effect Predictor (VEP)](https://www.ensembl.org/info/docs/tools/vep/index.html)).
+  - **<input_vep>**: The unfiltered output of VEP including annotations for all possible transcripts.
+
+- **<mut_profile>** (`optional`): Dictionary including the normalized frequencies of mutations (*values*) in every possible trinucleotide context (*keys*), such as 'ACA>A', 'ACC>A', and so on.
+
+> [!NOTE]
+> Examples of the input files are available in the [Test Input Folder](test/input).  
+Please refer to these examples to understand the expected format and structure of the input files.
+
+<!-- -->
+
+> [!NOTE]
+> Oncodrive3D uses the mutational profile of the cohort to build an accurate background model. However, it’s not strictly required. If the mutational profile is not provided, the tool will use a simple uniform distribution as the background model for simulating mutations and scoring potential 3D clusters.
+
+### Main Output
+
+- **Gene-level output**: CSV file (`<cohort>.3d_clustering_genes.csv`) containing the results of the analysis at the gene level. Each row represents a gene, sorted from the most significant to the least significant based on the 3D clustering analysis. The table also includes genes that were not analyzed, with the reason for exclusion provided in the `status` column.
+  
+- **Residue-level output**: CSV file (`<cohort>.3d_clustering_pos.csv`) containing the results of the analysis at the level of mutated residues. Each row corresponds to a mutated position within a gene and includes detailed information for each potential mutational cluster.
+
+### Usage
+
+```text
+Usage: oncodrive3d run [OPTIONS]
+
+Examples:
+  Basic run:
+    oncodrive3d run -i <input_maf> -p <mut_profile> -d <build_folder> -C <cohort_name>
+
+  Run using VEP output as input and MANE Select transcripts:
+    oncodrive3d run -i <input_vep> -p <mut_profile> -d <build_folder> -C <cohort_name> \
+                    --o3d_transcripts --use_input_symbols --mane
+```
+
+See `oncodrive3d run --help` for all options.
+
+> [!WARNING]
+> Human datasets built with the default settings pin canonical transcript metadata to the January 2024 Ensembl archive (release 111 / GENCODE v45). Annotate input variants with the same Ensembl/GENCODE release to avoid transcript-ID mismatches.
+
+<!-- -->
+
+> [!TIP]
+> To maximize the number of matching transcripts between your input mutations and Oncodrive3D's structures, supply the unfiltered VEP output as input along with `--o3d_transcripts --use_input_symbols`.
+
+### Handling Heterogeneous Sequencing Depth
+
+Oncodrive3D can ingest **site-specific mutability tables** when a single mutational profile is not representative of the cohort (e.g., mutation calling performed on highly heterogeneous-depth datasets such as ultra depth **Duplex sequencing** panels commonly used in normal tissue analysis). Provide an indexed TSV describing per-site mutability together with a JSON config via `--mutability_config_path`. The run automatically switches from trinucleotide rates to per-position probabilities and tracks additional diagnostics (`Mut_zero_mut_prob`, `Pos_zero_mut_prob`, status `Mut_with_zero_prob/No_mutability`).  
+
+Please see the [Mutability-aware runs guide](docs/mutability.md) for the expected file formats, config schema, and troubleshooting tips.
+
+### 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:
+
+| Variant | Tags | Approx size | Supported commands |
+| --- | --- | --- | --- |
+| Light | `bbglab/oncodrive3d:latest`, `:light`, `:<version>`, `:<version>-light` | ~490 MB | `run`, `plot` |
+| ChimeraX | `bbglab/oncodrive3d:chimerax`, `:<version>-chimerax` | ~1.6 GB | `run`, `plot`, `chimerax-plot` |
+| Full | `bbglab/oncodrive3d:full`, `:<version>-full` | ~4.7 GB | `run`, `plot`, `chimerax-plot`, `build-datasets`, `build-annotations` |
+
+#### Docker
+
+```bash
+docker pull bbglab/oncodrive3d:latest
+docker run --rm -v "$PWD":/data bbglab/oncodrive3d:latest \
+    oncodrive3d run -i /data/<input_maf> -p /data/<mut_profile> \
+                    -d /data/<build_folder> -C <cohort_name> -o /data/<output_dir>
+```
+
+#### Singularity
+
+```bash
+singularity pull oncodrive3d.sif docker://bbglab/oncodrive3d:latest
+singularity exec oncodrive3d.sif oncodrive3d run \
+    -i <input_maf> -p <mut_profile> -d <build_folder> -C <cohort_name>
+```
+
+> [!NOTE]
+> Singularity only auto-binds `$HOME` and `$PWD`. If any input or output path lives outside those (e.g. `/data/...` on a cluster), bind that host path explicitly with `-B /path:/path` (e.g. `singularity exec -B /data:/data oncodrive3d.sif ...`).
+
+### Testing
+
+To verify that Oncodrive3D is installed and configured correctly, you can perform a test run using the provided test input files:
+
+```bash
+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](docs/annotations_plotting.md) for prerequisites, usage examples, and output descriptions.
+
+## Parallel Processing on Multiple Cohorts
+
+Oncodrive3D ships with a [Nextflow](https://www.nextflow.io/) pipeline for running multiple cohorts in parallel. See the [Oncodrive3D Pipeline documentation](oncodrive3d_pipeline/README.md) for setup, input layout, and options.
+
+## License
+
+Oncodrive3D is available to the general public subject to certain conditions described in its [LICENSE](LICENSE).
+
+## Credits
+
+Oncodrive3D was originally written by Stefano Pellegrini.
+
+We thank the following people for their assistance in the development of this tool:
+
+- [@koszulordie](https://github.com/koszulordie)
+- [@FedericaBrando](https://github.com/FedericaBrando)
+- [@FerriolCalvet](https://github.com/FerriolCalvet)
+- [@odove](https://github.com/odove)
+
+## Citation
+
+If you use Oncodrive3D in your research, please cite:
+
+> **Oncodrive3D: fast and accurate detection of structural clusters of somatic mutations under positive selection**
+>
+> Stefano Pellegrini, Olivia Dove-Estrella, Ferran Muiños, Nuria Lopez-Bigas, Abel Gonzalez-Perez
+>
+> *Nucleic Acids Research* 53(15) (2025) doi:[10.1093/nar/gkaf776](https://doi.org/10.1093/nar/gkaf776)

oncodrive3d-1.0.9/README.md

@@ -0,0 +1,227 @@
+# 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.
+
+[![License: AGPL v3](https://img.shields.io/badge/License-AGPL_v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)
+[![docker](https://img.shields.io/docker/v/bbglab/oncodrive3d?logo=docker)](https://hub.docker.com/r/bbglab/oncodrive3d)
+[![PyPI - Version](https://img.shields.io/pypi/v/oncodrive3d?logo=pypi)](https://pypi.org/project/Oncodrive3D/)
+
+![Graphical abstract of Oncodrive3D](docs/images/graphical_abstract.png "Oncodrive3D")
+
+## Requirements
+
+Python 3.10+ is required. Some systems also need a C/C++ toolchain:
+
+- With sudo privileges:
+
+   ```bash
+   sudo apt install build-essential
+   ```
+
+- On HPC clusters, [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) (or [Mamba](https://mamba.readthedocs.io/en/latest/)) is recommended:
+
+   ```bash
+   conda create -n o3d python=3.10.0
+   conda activate o3d
+   conda install -c conda-forge gxx gcc libxcrypt clang zlib
+   ```
+
+## Installation
+
+- Install via PyPI:
+
+   ```bash
+   pip install oncodrive3d
+   ```
+
+- Alternatively, you can obtain the latest code from the repository and install it for development with pip:
+
+   ```bash
+   git clone https://github.com/bbglab/oncodrive3d.git
+   cd oncodrive3d
+   pip install -e .
+   oncodrive3d --help
+   ```
+
+- Or you can use a modern build tool like [uv](https://github.com/astral-sh/uv):
+
+   ```bash
+   git clone https://github.com/bbglab/oncodrive3d.git
+   cd oncodrive3d
+   uv run oncodrive3d --help
+   ```
+
+## Building Datasets
+
+This step builds the datasets necessary for Oncodrive3D to run the 3D clustering analysis. It is required once after installation or whenever you need to generate datasets for a different organism or apply a specific threshold to define amino acid contacts.
+
+> [!WARNING]
+> This step is time- and resource-intensive: it downloads and processes large amounts of structural data. Ensure adequate disk space, CPU, and a reliable internet connection (AlphaFold, Ensembl, Pfam, and other resources are fetched on demand).
+
+<!-- -->
+
+> [!WARNING]
+> MANE builds force AlphaFold DB v4 structures (non-MANE builds default to v6). PAE files for v4 are no longer hosted after 2025, so MANE builds without `--custom_pae_dir` fall back to binary contact maps. To keep PAE-weighted probability maps, supply precomputed v4 PAE files via `--custom_pae_dir`.
+
+<!-- -->
+
+> [!NOTE]
+> The first time that you run Oncodrive3D building dataset step with a given reference genome, it will download it from our servers. By default the downloaded datasets go to `~/.bgdata`. If you want to move these datasets to another folder you have to define the system environment variable `BGDATA_LOCAL` with an export command.
+
+```text
+Usage: oncodrive3d build-datasets [OPTIONS]
+
+Examples:
+  Basic build (human):
+    oncodrive3d build-datasets -o <build_folder>
+
+  Build with MANE Select transcripts:
+    oncodrive3d build-datasets -o <build_folder> --mane
+
+  Build mouse datasets:
+    oncodrive3d build-datasets -o <build_folder> -s mouse
+```
+
+See `oncodrive3d build-datasets --help` for all options.
+
+For more information on the output of this step, please refer to the [Building Datasets Output Documentation](docs/build_output.md).
+
+> [!TIP]
+> To extend MANE Select structural coverage beyond the AlphaFold MANE bundle, see the [MANE Preprocessing Toolkit](tools/preprocessing/README.md).
+
+## Running 3D Clustering Analysis
+
+See the [Input and Output Documentation](docs/run_input_output.md) for details on inputs and outputs.
+
+### Input
+
+- **Mutations file** (`required`): It can be either:
+  - **<input_maf>**: A Mutation Annotation Format (MAF) file annotated with consequences (e.g., by using [Ensembl Variant Effect Predictor (VEP)](https://www.ensembl.org/info/docs/tools/vep/index.html)).
+  - **<input_vep>**: The unfiltered output of VEP including annotations for all possible transcripts.
+
+- **<mut_profile>** (`optional`): Dictionary including the normalized frequencies of mutations (*values*) in every possible trinucleotide context (*keys*), such as 'ACA>A', 'ACC>A', and so on.
+
+> [!NOTE]
+> Examples of the input files are available in the [Test Input Folder](test/input).  
+Please refer to these examples to understand the expected format and structure of the input files.
+
+<!-- -->
+
+> [!NOTE]
+> Oncodrive3D uses the mutational profile of the cohort to build an accurate background model. However, it’s not strictly required. If the mutational profile is not provided, the tool will use a simple uniform distribution as the background model for simulating mutations and scoring potential 3D clusters.
+
+### Main Output
+
+- **Gene-level output**: CSV file (`<cohort>.3d_clustering_genes.csv`) containing the results of the analysis at the gene level. Each row represents a gene, sorted from the most significant to the least significant based on the 3D clustering analysis. The table also includes genes that were not analyzed, with the reason for exclusion provided in the `status` column.
+  
+- **Residue-level output**: CSV file (`<cohort>.3d_clustering_pos.csv`) containing the results of the analysis at the level of mutated residues. Each row corresponds to a mutated position within a gene and includes detailed information for each potential mutational cluster.
+
+### Usage
+
+```text
+Usage: oncodrive3d run [OPTIONS]
+
+Examples:
+  Basic run:
+    oncodrive3d run -i <input_maf> -p <mut_profile> -d <build_folder> -C <cohort_name>
+
+  Run using VEP output as input and MANE Select transcripts:
+    oncodrive3d run -i <input_vep> -p <mut_profile> -d <build_folder> -C <cohort_name> \
+                    --o3d_transcripts --use_input_symbols --mane
+```
+
+See `oncodrive3d run --help` for all options.
+
+> [!WARNING]
+> Human datasets built with the default settings pin canonical transcript metadata to the January 2024 Ensembl archive (release 111 / GENCODE v45). Annotate input variants with the same Ensembl/GENCODE release to avoid transcript-ID mismatches.
+
+<!-- -->
+
+> [!TIP]
+> To maximize the number of matching transcripts between your input mutations and Oncodrive3D's structures, supply the unfiltered VEP output as input along with `--o3d_transcripts --use_input_symbols`.
+
+### Handling Heterogeneous Sequencing Depth
+
+Oncodrive3D can ingest **site-specific mutability tables** when a single mutational profile is not representative of the cohort (e.g., mutation calling performed on highly heterogeneous-depth datasets such as ultra depth **Duplex sequencing** panels commonly used in normal tissue analysis). Provide an indexed TSV describing per-site mutability together with a JSON config via `--mutability_config_path`. The run automatically switches from trinucleotide rates to per-position probabilities and tracks additional diagnostics (`Mut_zero_mut_prob`, `Pos_zero_mut_prob`, status `Mut_with_zero_prob/No_mutability`).  
+
+Please see the [Mutability-aware runs guide](docs/mutability.md) for the expected file formats, config schema, and troubleshooting tips.
+
+### 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:
+
+| Variant | Tags | Approx size | Supported commands |
+| --- | --- | --- | --- |
+| Light | `bbglab/oncodrive3d:latest`, `:light`, `:<version>`, `:<version>-light` | ~490 MB | `run`, `plot` |
+| ChimeraX | `bbglab/oncodrive3d:chimerax`, `:<version>-chimerax` | ~1.6 GB | `run`, `plot`, `chimerax-plot` |
+| Full | `bbglab/oncodrive3d:full`, `:<version>-full` | ~4.7 GB | `run`, `plot`, `chimerax-plot`, `build-datasets`, `build-annotations` |
+
+#### Docker
+
+```bash
+docker pull bbglab/oncodrive3d:latest
+docker run --rm -v "$PWD":/data bbglab/oncodrive3d:latest \
+    oncodrive3d run -i /data/<input_maf> -p /data/<mut_profile> \
+                    -d /data/<build_folder> -C <cohort_name> -o /data/<output_dir>
+```
+
+#### Singularity
+
+```bash
+singularity pull oncodrive3d.sif docker://bbglab/oncodrive3d:latest
+singularity exec oncodrive3d.sif oncodrive3d run \
+    -i <input_maf> -p <mut_profile> -d <build_folder> -C <cohort_name>
+```
+
+> [!NOTE]
+> Singularity only auto-binds `$HOME` and `$PWD`. If any input or output path lives outside those (e.g. `/data/...` on a cluster), bind that host path explicitly with `-B /path:/path` (e.g. `singularity exec -B /data:/data oncodrive3d.sif ...`).
+
+### Testing
+
+To verify that Oncodrive3D is installed and configured correctly, you can perform a test run using the provided test input files:
+
+```bash
+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](docs/annotations_plotting.md) for prerequisites, usage examples, and output descriptions.
+
+## Parallel Processing on Multiple Cohorts
+
+Oncodrive3D ships with a [Nextflow](https://www.nextflow.io/) pipeline for running multiple cohorts in parallel. See the [Oncodrive3D Pipeline documentation](oncodrive3d_pipeline/README.md) for setup, input layout, and options.
+
+## License
+
+Oncodrive3D is available to the general public subject to certain conditions described in its [LICENSE](LICENSE).
+
+## Credits
+
+Oncodrive3D was originally written by Stefano Pellegrini.
+
+We thank the following people for their assistance in the development of this tool:
+
+- [@koszulordie](https://github.com/koszulordie)
+- [@FedericaBrando](https://github.com/FedericaBrando)
+- [@FerriolCalvet](https://github.com/FerriolCalvet)
+- [@odove](https://github.com/odove)
+
+## Citation
+
+If you use Oncodrive3D in your research, please cite:
+
+> **Oncodrive3D: fast and accurate detection of structural clusters of somatic mutations under positive selection**
+>
+> Stefano Pellegrini, Olivia Dove-Estrella, Ferran Muiños, Nuria Lopez-Bigas, Abel Gonzalez-Perez
+>
+> *Nucleic Acids Research* 53(15) (2025) doi:[10.1093/nar/gkaf776](https://doi.org/10.1093/nar/gkaf776)