-
Notifications
You must be signed in to change notification settings - Fork 0
/
mkdocs.yml
116 lines (105 loc) · 3.49 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
site_name: FedPyDESeq2
site_url: https://github.com/owkin/fedpydeseq2
site_author: Boris Muzellec, Ulysse Marteau-Ferey, Tangy Marchand
site_description: "A federated learning implementation of DESeq2 for differential expression analysis."
repo_name: owkin/fedpydeseq2
repo_url: https://github.com/owkin/fedpydeseq2
copyright: Copyright (c) 2024-present Owkin Inc.
theme:
name: material
palette:
primary: indigo
accent: indigo
scheme: default
toggle:
icon: material/toggle-switch-off-outline
name: Switch to dark mode
dark:
scheme: slate
toggle:
icon: material/toggle-switch
name: Switch to light mode
font:
text: Roboto
code: Roboto Mono
features:
- content.code.copy
- content.tabs.link
- palette.switch
markdown_extensions:
- pymdownx.highlight:
anchor_linenums: true
line_spans: __span
pygments_lang_class: true
- pymdownx.arithmatex:
generic: true
- pymdownx.inlinehilite
- pymdownx.snippets
- admonition
- pymdownx.details
- pymdownx.superfences
- attr_list
- md_in_html
- tables
- pymdownx.tabbed:
alternate_style: true
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
- footnotes
extra_javascript:
- javascripts/katex.js
- https://unpkg.com/katex@0/dist/katex.min.js
- https://unpkg.com/katex@0/dist/contrib/auto-render.min.js
extra_css:
- https://unpkg.com/katex@0/dist/katex.min.css
plugins:
- search:
- git-revision-date-localized:
type: timeago
enable_creation_date: true
- mkdocstrings:
handlers:
python:
options:
docstring_style: numpy
docstring_section_style: table
docstring_options:
ignore_init_summary: false
merge_init_into_class: false
- bibtex:
bib_file: "./docs/references.bib"
- include-markdown:
extra:
social:
- icon: fontawesome/brands/github
link: https://github.com/owkin/fedpydeseq2
nav:
- General:
- Home: index.md
- Installation: usage/installation.md
- Contributing: usage/contributing.md
- References: usage/references.md
- API:
- Home: api/index.md
- Running an experiment: api/fedpydeseq2_pipeline.md
- Core:
- Home: api/core/deseq2_core/index.md
- Build design matrix: api/core/deseq2_core/build_design_matrix.md
- Compute size factors: api/core/deseq2_core/compute_size_factors.md
- Estimating LFCs and dispersions: api/core/deseq2_core/deseq2_lfc_dispersions.md
- Computing the Cooks distance: api/core/deseq2_core/compute_cook_distance.md
- Replacing outliers: api/core/deseq2_core/replace_outliers.md
- Replace refitted values: api/core/deseq2_core/replace_refitted_values.md
- Computing statistics and p-values: api/core/deseq2_core/deseq2_stats.md
- Saving results: api/core/deseq2_core/save_pipeline_results.md
- Strategy: api/core/strategy.md
- Utils:
- Core: api/core/utils.md
- Substra: api/substra_utils.md
- Federated algorithms:
- Home: api/core/federated_algorithms/index.md
- Compute trimmed mean: api/core/federated_algorithms/compute_trimmed_mean.md
- Compute dispersions with grid search: api/core/federated_algorithms/dispersions_grid_search.md
- Federated IRLS: api/core/federated_algorithms/fed_irls.md
- Federated ProxQuasiNewton: api/core/federated_algorithms/fed_pqn.md