README.md

SelectSim_analysis

Description

• The github repos consist of scripts to perform the analysis related to SelectSim paper.
• The contents of the repository is mentioned below.

  ├── analysis
  │   ├── catalogue
  │   │   └── notebook
  │   │       ├── catalouge_consistent.ipynb
  │   │       ├── dfci_merge_results.ipynb
  │   │       ├── dfci_runs.ipynb
  │   │       ├── merge_all_results.ipynb
  │   │       ├── msk_merge_results.ipynb
  │   │       ├── msk_runs.ipynb
  │   │       ├── tcga_merge_results.ipynb
  │   │       └── tcga_runs.ipynb
  │   ├── normal_mutation
  │   │   ├── notebook
  │   │   │   └── data_processing.ipynb
  │   │   └── run_selectSim.r
  │   ├── primary_met
  │   │   └── notebook
  │   │       ├── data_processing.ipynb
  │   │       ├── msk_p_m_enrichment.ipynb
  │   │       ├── msk_p_m_gene_frequency.ipynb
  │   │       └── msk_p_m_runs.ipynb
  │   ├── primary_met_elastic_net
  │   │   ├── EN_functions.r
  │   │   └── run_EN.r
  │   └── roubustness_benchmarking
  │       ├── coselens.r
  │       ├── notebook
  │       │   ├── cooccur.ipynb
  │       │   ├── Discover.ipynb
  │       │   ├── Discover_SelectSim.ipynb
  │       │   ├── GamTOC.ipynb
  │       │   ├── MCC.ipynb
  │       │   ├── mutational_load.ipynb
  │       │   ├── sampling_recovery.ipynb
  │       │   ├── select.ipynb
  │       │   ├── SelectSim.ipynb
  │       │   ├── tcga_robustness_analysis.ipynb
  │       │   └── WeSME_CO.ipynb
  │       └── time_analysis_berewire_simulation.r
  ├── data_processing
  │   └── notebook
  │       ├── genie_data_processing.ipynb
  │       ├── msk_dfci_gam_create.ipynb
  │       ├── msk_dfci_sample_filtering_annotation.ipynb
  │       └── tcga_gam_create.ipynb
  └── README.md
  

• The analysis folder consists of scripts (jupyter R-notebooks and .R script) files related to different analysis (catalogue, normal mutation, primary vs metastasis etc.)
• The data processing folder consists of scripts (jupyter R-notebooks) to process the data to generate the SelectSim algorithm input run objects.

Data Availablity

• Data needed for the scripts are avialabe from zenodo and zenodo on request.

SelectSim Algorithm

• SelectSim algorithm is avilable from github.

Who do I talk to?

• For any bugs or feature support in using SelectSim, please use the issue tracker.
• For any other question related to SelectSim, please contact Prof Giovanni Ciriello ([email protected]) or Arvind Iyer ([email protected]).