_pkgdown.yml

url: http://hectorrdb.github.io//condimentsPaper

template:
  params:
    bootswatch: flatly

home:
  title: "condiments Paper"
  type: inverse


navbar:
  right:
   - icon: fa-github
     href: https://github.com/HectorRDB/condimentsPaper

reference:
  - title: "Download the datasets for the case studies"
    desc: >
      Those three functions obtain the dataset and metadata (mostly from GEO) 
      and format them for analysis.
    contents:
      - '`import_fibrosis`'
      - '`import_KRAS`'
      - '`import_TCDD`'
      - '`import_TGFB`'
  - title: "Case study datasets"
    desc: >
      The formatted datasets used in the simulations
    contents:
      - '`condRes_monocle`'
      - '`fibrosis`'
      - '`kras`'
      - '`tcdd`'
      - '`tgfb`'
  - title: "Simulations"
    desc: >
      All functions needed to run or analyze the simulations
    contents:
      - '`all_metrics`'
      - '`anayze_all`'
      - '`anayze_all_per_cond`'
      - '`anayze_multiple_conditions`'
      - '`create_5_lineages_simu`'
      - '`create_bifurcating_simu`'
      - '`create_bifurcating_three_conditions_simu`'
      - '`create_consecutive_bifurcating_simu`'
  - title: 'Visualization'
    desc: "Functions to plot the results"
    contents:
      - '`plot_backbone_modulenet_simplify`'
      - '`plot_example`'
      - '`plot_reduced_dim`'
      - '`plot_reduced_dim_together`'
  - title: 'Simulation data'
    desc: "The simulation results and examples"
    contents:
      - '`complex`'
      - '`complex_sce`'
      - '`five_lins`'
      - '`fivelin_sce`'
      - '`fork`'
      - '`fork_sce`'
      - '`step1_fail`'
      - '`tree`'
      - '`tree_sce`'
      - '`unstability`'