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https://github.com/bbglab/boostdm-analyses

Source code to reproduce the figures of the boostDM paper

https://github.com/bbglab/boostdm-analyses

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (2.4%) to scientific vocabulary

Keywords

cancer-genes drivers mutations
Last synced: 5 months ago · JSON representation

Repository

Source code to reproduce the figures of the boostDM paper

Basic Info
  • Host: GitHub
  • Owner: bbglab
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 32.1 MB
Statistics
  • Stars: 5
  • Watchers: 8
  • Forks: 2
  • Open Issues: 0
  • Releases: 0
Topics
cancer-genes drivers mutations
Created almost 5 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

boostDM manuscript analyses

Source code to reproduce the figures of the paper:

In silico saturation mutagenesis of cancer genes
Ferran Muiños, Francisco Martinez-Jimenez, Oriol Pich, Abel Gonzalez-Perez, Nuria Lopez-Bigas
DOI: https://doi.org/10.1038/s41586-021-03771-1

Content

This repo contains the source code to reproduce the main and extended figures of the paper.
Each figure has its own jupyter notebook to render the figure's panels.

Main figures

Figure 1: [ipynb] [pdf]
Figure 2: [ipynb] [pdf]
Figure 3: [ipynb] [pdf]
Figure 4: [ipynb] [pdf]

Extended Figures

Extended Figure 1: [ipynb] [pdf]
Extended Figure 2: [ipynb] [pdf]
Extended Figure 3: [ipynb] [pdf]
Extended Figure 4: [ipynb] [pdf]
Extended Figure 5: [ipynb] [pdf]
Extended Figure 6: [ipynb] [pdf]
Extended Figure 7: [ipynb] [pdf]
Extended Figure 8: [ipynb] [pdf]
Extended Figure 9: [ipynb] [pdf]

Complementary content

You can access to boostDM source code and documentation in the boostDM pipeline repository.
You can explore and download the main outputs of boostDM in the boostDM website.

Requirements

Download source data

All the code features in this repo feeds on source data.

Make sure that you download a stable copy of the source data from zenodo and keep it in the root of the repo from zenodo as follows:

$ pip install zenodo_get $ bash get.sh $ tar -xvf source-data/source-data-zenodo.tar.gz $ cp -r source-data/boostdm-analyses .

Run notebooks with singularity

The notebooks must be run on a jupyter-notebook or jupyter-lab session launched from Singularity image that already satisfies all the dependencies for the notebooks to run.

Follow these steps:

  • Install the latest Singularity release

  • Create a singularity image using the Singularity recipe:

$ sudo singularity build boostdm-analyses.sif Singularity

  • Now you can run the notebooks from singularity:

$ singularity exec boostdm-analyses.sif jupyter-lab

Owner

  • Name: BBGLab - Barcelona Biomedical Genomics Lab
  • Login: bbglab
  • Kind: organization
  • Email: bbglab@irbbarcelona.org
  • Location: Barcelona

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