NanoQuRe/_pkgdown.yml at master · LRB-IIMCB/NanoQuRe · 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
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
url: https://LRB-IIMCB.github.io/NanoQuRe/

template:
  bootstrap: 5
  bootswatch: flatly
  theme: arrow-light
  bslib:
    primary: "#612a78"
    link-color: "#612a78"
    navbar-bg: "#612a78"
    heading-color: "#612a78"
  includes:
    in_header: |
      <style>
      /* Unify fonts: system font stack throughout */
      body, .contents, .contents p, .contents li,
      .contents table, .contents th, .contents td {
        font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto,
                     "Helvetica Neue", Arial, sans-serif;
        font-size: 1rem;
        line-height: 1.5;
      }

      /* Consistent table styling */
      .contents table {
        font-size: 0.95rem;
        border-collapse: collapse;
        width: 100%;
        margin-bottom: 1rem;
      }

      .contents th, .contents td {
        padding: 0.5rem 0.75rem;
        border: 1px solid #dee2e6;
        vertical-align: top;
      }

      .contents th {
        background-color: #f8f9fa;
        font-weight: 600;
      }

      /* Consistent code styling */
      .contents code {
        font-family: SFMono-Regular, Menlo, Monaco, Consolas,
                     "Liberation Mono", "Courier New", monospace;
        font-size: 0.875em;
        padding: 0.125rem 0.25rem;
        background-color: #f8f9fa;
        border-radius: 0.25rem;
      }
      </style>

home:
  title: "NanoQuRe — Quality Control for Oxford Nanopore Sequencing"
  description: >
    An R package for quality control of Oxford Nanopore sequencing data.
    Generates interactive plots, summary tables, and self-contained HTML
    reports from ONT sequencing summary files.
  sidebar:
    structure: [links, license, citation, authors, dev]

navbar:
  bg: primary
  structure:
    left: [intro, reference, articles]
    right: [search, github]
  components:
    intro:
      text: "Get Started"
      href: articles/getting-started.html
    articles:
      text: "Vignettes"
      menu:
        - text: "Getting Started"
          href: articles/getting-started.html
        - text: "Using Individual Functions"
          href: articles/individual-functions.html
    github:
      icon: fab fa-github
      href: https://github.com/LRB-IIMCB/NanoQuRe
      aria-label: GitHub

reference:
  - title: "Report Generation"
    desc: "Generate a full HTML QC report"
    contents:
      - generate_report

  - title: "Summary Tables"
    desc: "Functions that return summary data frames"
    contents:
      - sequencing_stats
      - quality_stats
      - calculate_n50

  - title: "Yield & Throughput Plots"
    desc: "Plots showing sequencing output over time"
    contents:
      - plot_cumulative_yield
      - plot_seq_throughput
      - plot_average_speed

  - title: "Quality & Length Plots"
    desc: "Plots showing read quality and length distributions"
    contents:
      - plot_read_lengths
      - plot_quality_distribution

  - title: "Channel Activity Plots"
    desc: "Plots showing pore and channel behaviour"
    contents:
      - plot_active_channels
      - pore_activity_heatmap
      - plot_double

  - title: "Example Data"
    desc: "Bundled dataset for examples and vignettes"
    contents:
      - sample_data

  - title: "Package"
    contents:
      - NanoQuRe-package

footer:
  structure:
    left: developed_by
    right: built_with

news:
  one_page: true
  cran_dates: false