SelectSim/_pkgdown.yml at main · CSOgroup/SelectSim · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
url: https://csogroup.github.io/SelectSim/

template:
  bootstrap: 5
  bootswatch: journal

home:
  title: "SelectSim — Evolutionary dependencies in cancer"
  sidebar:
    structure: [links, license, citation, authors, dev]

navbar:
  logo:
    src: logo.svg
    alt: SelectSim
    width: 30
    href: https://csogroup.github.io/SelectSim/
  structure:
    left:  [intro, reference, articles, news]
    right: [github]
  components:
    intro:
      text: "Get started"
      href: articles/introduction.html
    github:
      icon: fab fa-github
      href: https://github.com/CSOgroup/SelectSim
      aria-label: GitHub

reference:
  - title: "Main interface"
    desc: "End-to-end analysis: run the full SelectSim pipeline in one call."
    contents:
      - selectX

  - title: "Core workflow"
    desc: >
      Step-by-step building blocks called internally by `selectX`. Expose
      these directly for custom pipelines or debugging.
    contents:
      - new.AL.general
      - get.blocks
      - template.obj.gen
      - generateS
      - generateW_block
      - generateW_mean_tmb
      - null_model_parallel
      - retrieveOutliers

  - title: "Statistics"
    desc: "Overlap computation, effect sizes, FDR estimation, and results table."
    contents:
      - new.ALS
      - new.AMS
      - al.stats
      - am.stats
      - al.pairwise.alteration.stats
      - am.pairwise.alteration.overlap
      - am.pairwise.alteration.coverage
      - am.weight.pairwise.alteration.overlap
      - r.am.pairwise.alteration.overlap
      - w.r.am.pairwise.alteration.overlap
      - binary.yule
      - effectSize
      - r.effectSize
      - add
      - estimateFDR2
      - estimate_p_val
      - estimate_pairwise_p
      - interaction.table

  - title: "Data processing"
    desc: "MAF file filtering utilities and gene alteration matrix (GAM) construction."
    contents:
      - maf2gam
      - starts_with("filter_maf")
      - starts_with("stat_maf")
      - mutation_type
      - TCGA_maf_schema
      - GENIE_maf_schema

  - title: "Visualization"
    desc: "Plot helpers for inspecting results and null model distributions."
    contents:
      - obs_exp_scatter
      - ridge_plot_ed
      - ridge_plot_ed_compare
      - overlap_pair_extract
      - theme_Publication

  - title: "Datasets"
    desc: "Example datasets bundled with the package."
    contents:
      - luad_run_data
      - luad_result
      - luad_maf
      - oncokb_genes
      - oncokb_truncating_genes
      - variant_catalogue

articles:
  - title: "Vignettes"
    navbar: ~
    contents:
      - introduction
      - data_processing

footer:
  structure:
    left:  developed_by
    right: built_with