-
Notifications
You must be signed in to change notification settings - Fork 0
/
mkdocs.yml
149 lines (149 loc) · 5.64 KB
/
mkdocs.yml
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
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
site_name: GeneWeaver
theme:
name: material
logo: assets/GW2-logo.png
favicon: assets/GW2-logo.png
icon:
repo: fontawesome/brands/git-alt
font:
text: Roboto
code: Roboto Mono
palette:
- scheme: geneweaver
media: "(prefers-color-scheme: light)"
toggle:
icon: material/toggle-switch-off-outline
name: Switch to dark mode
- scheme: slate
media: "(prefers-color-scheme: dark)"
primary: blue grey
accent: blue
toggle:
icon: material/toggle-switch
name: Switch to light mode
features:
- navigation.instant
- navigation.tracking
# - navigation.tabs
- navigation.sections
# - navigation.expand
- navigation.indexes
# - navigation.tabs.sticky
# - header.autohide
- navigation.footer
- search.suggest
- search.highlight
- content.tabs.link
extra_css:
- stylesheets/extra.css
repo_name: TheJacksonLaboratory/geneweaver-docs
repo_url: https://github.com/TheJacksonLaboratory/geneweaver-docs
edit_uri: edit/main/docs/
extra:
generator: true
social:
- icon: fontawesome/brands/github
link: https://github.com/orgs/TheJacksonLaboratory/repositories?q=geneweaver
name: GitHub Repositories
- icon: fontawesome/brands/python
link: https://pypi.org/search/?q=geneweaver
name: Python Packages
- icon: material/web
link: https://geneweaver.org
name: Geneweaver Website
- icon: material/api
link: https://geneweaver.jax.org/api/docs
name: Geneweaver API
copyright: These pages are maintained by the GeneWeaver team and the Chesler Lab at The Jackson Laboratory in Bar Harbor, Maine.
markdown_extensions:
- admonition
- tables
- pymdownx.details
- pymdownx.superfences
- attr_list
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
- md_in_html
- pymdownx.superfences
- def_list
- footnotes
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.tabbed:
alternate_style: true
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
plugins:
- search
- mkdocs-jupyter:
include_source: True
nav:
- Home: index.md
- Getting Started:
- getting-started/index.md
- Foundational Concepts: getting-started/foundational-concepts.md
- Web Application: getting-started/web-application.md
- Command Line Interface: getting-started/command-line-interface.md
- Running Tools Locally: getting-started/running-tools-locally.md
# - Contributing to Packages: getting-started/contributing-to-packages.md
# - Contributing to Documentation: getting-started/contributing-to-documentation.md
- Concepts:
- concepts/index.md
- Genes and GeneSets: concepts/genes-and-genesets.md
- External Source Data: concepts/geneweaver-data.md
- Geneweaver Data Model: concepts/geneweaver-data-model.md
- Package Based Architecture: concepts/package-based-architecture.md
- Tutorial:
- tutorial/index.md
- Client Login: tutorial/geneweaver_client_login.ipynb
- Map Gene IDs: tutorial/map-gene-ids.ipynb
- Finding Genesets: tutorial/finding-genesets.ipynb
- NCI-60 Example Workflow: tutorial/nci_60_example_01.ipynb
# - Geneweaver Command Line Interface:
# - tutorial/geneweaver_command_line.md
# - tutorial/geneweaver_command_line.md
# - Download Genesets (CLI): tutorial/downloading_geneset_command_line.md
# - Download Genesets: tutorial/download_genesets.ipynb
# - Accessing Geneweaver Data: tutorial/accessing-geneweaver-data.md
# - Running a Local Database: tutorial/running-a-local-database.md
# - Creating New Tools: tutorial/creating-new-tools.md
# - Testing New Tools: tutorial/testing-new-tools.md
# - Exploring Data in Javascript: tutorial/exploring-data-in-javascript.md
# - Creating Documentation Sites: tutorial/creating-a-new-documentation-site.md
- Reference:
- reference/index.md
- 'Analysis Tools':
- analysis-tools/index.md
- 'HiSim Graph': analysis-tools/hisim-graph.md
- 'GeneSet Graph': analysis-tools/geneset-graph.md
- 'Jaccard Similarity': analysis-tools/jaccard-similarity.md
- 'GeneSet Clustering': analysis-tools/clustering.md
- DBSCAN: analysis-tools/dbscan.md
- MSET: analysis-tools/mset.md
- 'ABBA Gene Search': analysis-tools/abba.md
- 'Boolean Algebra': analysis-tools/boolean-algebra.md
- 'Find Variants': analysis-tools/find-variants.md
- gweave (Command Line):
- reference/command-line/index.md
- Logging In: reference/command-line/logging-in.md
- API Commands: reference/command-line/api-commands.md
- GeneSet Tiers: reference/geneset-tiers.md
- GeneSet Utilities: reference/geneset-utilities.md
- Curation:
- reference/curation/index.md
- Standards: reference/curation/curation-standards.md
- Process: reference/curation/curation-process.md
- ReST API: reference/restful-api.md
- Available Packages: reference/available-packages.md
- Data Model: reference/data-model.md
- Contributing Guide: reference/contributing-guide.md
- Development Guide: reference/development-guide.md
- External Data Sources: reference/external-data-sources.md
- Publications: reference/publications.md
- License: reference/license.md
- Policies: reference/policies.md
- Acknowledgements: reference/acknowledgements.md