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mkdocs.yml
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site_name: Open-ST
site_url: https://open.st
site_author: Daniel León-Periñán, Lena Marie Schott
site_description: >-
Open-ST: Open-Source Spatial Transcriptomics
copyright: Copyright © 2024 Open-ST
repo_name: rajewsky-lab/openst
repo_url: https:/rajewsky-lab/openst
edit_uri: https:/rajewsky-lab/openst/edit/main/docs
nav:
- Home: index.md
- Step-by-step:
- Introduction: introduction.md
- Experimental:
- Getting started: experimental/getting_started.md
- Capture area generation: experimental/capture_area_generation.md
- Tissue processing and RNA quality control: experimental/tissue_processing_and_RNA_qc.md
- Library preparation: experimental/library_preparation.md
- Sequencing of Open-ST library: experimental/sequencing_of_openst_library.md
- Computational:
- Getting started: computational/getting_started.md
- Preprocessing capture area library: computational/preprocessing_capture_area.md
- Preprocessing transcriptomic library: computational/preprocessing_openst_library.md
- Pairwise alignment: computational/pairwise_alignment.md
- Segmentation and single-cell quantification: computational/generate_expression_matrix.md
- 3D reconstruction: computational/threed_reconstruction.md
- API: api.md
- FAQ: faq.md
- Examples:
- Getting started: examples/getting_started.md
- Dataset summary: examples/datasets.md
- Adult mouse hippocampus:
- Introduction: examples/adult_mouse/introduction.md
- Preprocessing transcriptomic library: examples/adult_mouse/preprocessing_sequencing.md
- Pairwise alignment: examples/adult_mouse/pairwise_alignment.md
- Segmentation and single-cell quantification: examples/adult_mouse/generate_expression_matrix.md
- Exploratory analysis (Jupyter): static/examples/notebooks/hypo_adult_eda.ipynb
- E13 mouse head:
- Introduction: examples/e13_mouse/introduction.md
- Preprocessing transcriptomic library: examples/e13_mouse/preprocessing_sequencing.md
- Pairwise alignment: examples/e13_mouse/pairwise_alignment.md
- Segmentation and single-cell quantification: examples/e13_mouse/generate_expression_matrix.md
- Exploratory analysis (Jupyter): static/examples/notebooks/e13_head_eda.ipynb
theme:
name: material
custom_dir: docs/theme_override_home
features:
- navigation.indexes
- navigation.sections
logo: static/logos/openst_logo_transparent_completeO.png
features:
- announce.dismiss
- content.action.edit
- content.action.view
- content.code.annotate
- content.code.copy
- content.tooltips
- navigation.footer
- navigation.indexes
- navigation.sections
- navigation.tabs
- navigation.path
- navigation.top
- navigation.tracking
- search.highlight
- search.share
- search.suggest
- toc.integrate
palette:
primary: custom
accent: custom
icon:
repo: fontawesome/brands/github
language: en
favicon: static/logos/openst_logo_transparent_completeO.png
plugins:
- search
- autorefs
- mknotebooks
extra:
copyright: Copyright © 2023 Open-ST
social:
- icon: fontawesome/brands/twitter
link: https://twitter.com/open_sts
name: Twitter
- icon: fontawesome/brands/github
link: https:/rajewsky-lab/openst
name: GitHub
- icon: fontawesome/brands/docker
name: Docker
link: https://hub.docker.com/u/rajewsky
version:
provider: mike
default: latest
markdown_extensions:
- abbr
- admonition
- attr_list
- def_list
- footnotes
- md_in_html
- toc:
permalink: true
- pymdownx.arithmatex:
generic: true
- pymdownx.betterem:
smart_enable: all
- pymdownx.caret
- pymdownx.details
- pymdownx.emoji:
emoji_generator: !!python/name:material.extensions.emoji.to_svg
emoji_index: !!python/name:material.extensions.emoji.twemoji
- pymdownx.highlight:
anchor_linenums: true
line_spans: __span
pygments_lang_class: true
- pymdownx.inlinehilite
- pymdownx.keys
- pymdownx.mark
- pymdownx.smartsymbols
- pymdownx.snippets:
auto_append:
- includes/mkdocs.md
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
- codehilite:
guess_lang: false
linenums: true
noclasses: false
use_pygments: true
- pymdownx.tabbed:
alternate_style: true
combine_header_slug: true
slugify: !!python/object/apply:pymdownx.slugs.slugify
kwds:
case: lower
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.tilde
extra_javascript:
- javascripts/katex.js
- https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.js
- https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/contrib/auto-render.min.js
extra_css:
- https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.css
- stylesheets/extra.css