_pkgdown.yml

url: caravagnalab.github.io/INCOMMON
template:
  bootstrap: 5

reference:
- title: Available data
  desc:  Datasets included in the package.
  contents:
  - MSK_genomic_data
  - MSK_clinical_data
  - pcawg_priors
  - cancer_gene_census
  - MSK_classified

- title: INCOMMON classification
  desc:  Main functions to classify mutations
  contents:
  - init
  - classify

- title: Visualisation
  desc: Functions to plot INCOMMON classification results
  contents:
  - plot_classification
  - print.INCOMMON
  - plot_class_fraction
  - plot_prior
  - plot_met_volcano
  - plot_tropism

- title: Getter Functions
  desc:  Functions to extract model information
  contents:
  - classification
  - parameters
  - priors
  - posterior


- title: INCOMMON Model
  desc: Functions to compute model likelihood and posterior distributions
  contents:
  - compute_likelihood
  - compute_posterior
  - genome_interpreter

- title: Survival analysis with INCOMMON classes
  desc: Functions to perform survival analysis with patient stratificaiton based on INCOMMON classes
  contents:
  - kaplan_meier_fit
  - cox_fit
  - plot_survival_analysis

- title: Metastatic pattern analysis with INCOMMON classes
  desc: Functions to perform metastatic propensity and tropism analysis with INCOMMON interpreted tumor genomes
  contents:
  - met_propensity
  - met_tropism