markeR/_pkgdown.yml at default · DiseaseTranscriptomicsLab/markeR · 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
url: https://diseasetranscriptomicslab.github.io/markeR/
template:
  bootstrap: 5
  light-switch: true
  assets: "pkgdown/assets"
  toc:
    depth: 4

badges: true

home:
  sidebar:
      structure: [links, license, community, citation, authors, dev]

reference:
  - title: "Package Help Page"
    contents:
      - markeR
  - title: "Example Data"
    contents:
      - counts_example
      - metadata_example
      - genesets_example
  - title: "Gene Set Similarity"
    contents:
      - geneset_similarity
  - title: "Score-based Analysis"
    contents:
      - CalculateScores
      - PlotScores
      - ROC_Scores
      - AUC_Scores
      - FPR_Simulation
  - title: "Enrichment-based Methods"
    contents:
      - calculateDE
      - plotVolcano
      - runGSEA
      - plotGSEAenrichment
      - plotNESlollipop
      - plotCombinedGSEA
  - title: "Variable Association (Discovery Mode)"
    contents:
      - VariableAssociation
  - title: "Visualization Functions"
    contents:
      - VisualiseIndividualGenes
      - IndividualGenes_Violins
      - CorrelationHeatmap
      - ExpressionHeatmap
      - ROCandAUCplot
      - CohenD_IndividualGenes
      - plotPCA