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mkdocs.yml
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mkdocs.yml
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site_name: "BEDbase: a unified platform for genomic regions"
theme:
logo: img/bedbase_logo.svg
favicon: img/bedbase_bug.svg
name: material
custom_dir: overrides
features:
- header.autohide
- navigation.sections
# - navigation.expand
- navigation.footer
- navigation.indexes
- toc.follow
- content.action.edit
- content.action.view
- navigation.tabs
- navigation.top
markdown_extensions:
- pymdownx.highlight:
use_pygments: true
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: "!!python/name:pymdownx.superfences.fence_code_format"
extra_css:
- stylesheets/extra.css
extra:
generator: false # turn off theme link
copyright: >
<a class="" href="http://databio.org/">
<img src="https://databio.org/images/logo/logo_databio_long.svg"
style="height:60px;"
alt="Databio logo">
</a>
nav:
- Home: README.md
- BEDbase:
- BEDbase: bedbase/README.md
- User guides:
- Public BEDbase UI user guide: bedbase/bedbase-ui-user-guide.md
- Public BEDbase API user guide: bedbase/bedbase-api-user-guide.md
- Developer guides:
- BEDhost API server:
- BEDhost overview: bedhost/README.md
- Building docker image: bedhost/build_image.md
- Deploy API: bedhost/deployment.md
- Changelog: bedhost/changelog.md
- BBConf configuration:
- BBConf: bbconf/README.md
- Configuring: bedboss/how-to-configure.md
- Overview: bbconf/overview.md
- Guide: bbconf/bbc_api.md
- Changelog: bbconf/changelog.md
- BEDBoss processing pipeline: ../bedboss
- Reference:
- How to cite: citations.md
- Usage: bedboss/usage.md
- Support: https://github.com/bedbase/bedboss/issues
- Contributing: contributing.md
- Changelog: changelog.md
- BEDboss:
- BEDboss: bedboss/README.md
- Tutorials:
- BEDboss run-pep: bedboss/tutorials/tutorial_run_pep.md
- BEDboss-all pipeline: bedboss/tutorials/tutorial_all.md
- BEDmaker tutorial: bedboss/tutorials/bedmaker_tutorial.md
- BEDqc tutorial: bedboss/tutorials/bedqc_tutorial.md
- BEDstat tutorial: bedboss/tutorials/bedstat_tutorial.md
- BEDbuncher tutorial: bedboss/tutorials/bedbuncher_tutorial.md
- BEDindex tutorial: bedboss/tutorials/bedindex_tutorial.md
- BEDclassifier tutorial: bedboss/tutorials/bedclassifier_tutorial.md
- How to guides:
- Create BEDbase database: bedboss/how-to-create-database.md
- Create config file: bedboss/how-to-configure.md
- Install dependencies: bedboss/how-to-install-requirements.md
- Reference:
- How to cite: citations.md
- Usage: bedboss/usage.md
- Changelog: bedboss/changelog.md
- Geniml:
- Geniml: geniml/README.md
- Getting Started:
- Module overviews: geniml/modules.md
- How-to guides:
- Cache BED files with BBClient: geniml/tutorials/bbclient.md
- Use BED cache in R: geniml/tutorials/pyBiocFileCache.md
- Tokenization: geniml/tutorials/tokenization.md
- Tokenize a BED file with CLI: geniml/tutorials/cli-tokenization.md
- Train region2vec embeddings: geniml/tutorials/region2vec.md
- Train BEDspace model:
- Train BEDSpace embeddings: geniml/tutorials/bedspace.md
- BEDspace results notebook: geniml/code/bedspace-analysis.md
- Use scEmbed model:
- Train single-cell embeddings: geniml/tutorials/train-scembed-model.md
- Populate a vector store: geniml/tutorials/load-qdrant-with-cell-embeddings.md
- Predict cell-types using KNN: geniml/tutorials/cell-type-annotation-with-knn.md
- Evaluate embeddings: geniml/tutorials/evaluation.md
- Create consensus peaks with CLI: geniml/tutorials/create-consensus-peaks.md
- Create consensus peaks with Python: geniml/code/create-consensus-peaks-python.md
- Assess universe fit: geniml/code/assess-universe.md
- Fine-tune embeddings: geniml/tutorials/fine-tune-region2vec-model.md
- Randomize bed files: geniml/tutorials/bedshift.md
- Create evaluation dataset with bedshift: geniml/tutorials/bedshift-evaluation-guide.md
- Create search backend: geniml/tutorials/text2bednn-search-interface.md
- Reference:
- How to cite: citations.md
- API documentation: geniml/autodoc_build/geniml.md
- Support: geniml/support.md
- Contributing: geniml/contributing.md
- Changelog: geniml/changelog.md
- Gtars:
- Gtars: gtars/README.md
- Manuscripts:
- How to cite: citations.md
- Published manuscripts:
- Gharavi et al. 2021: manuscripts/gharavi2021.md
- Gu et al. 2021: manuscripts/gu2021.md
- Rymuza et al. 2024: manuscripts/rymuza2024.md
- Gharavi et al. 2024: manuscripts/gharavi2024.md
- LeRoy et al. 2024: manuscripts/leroy2024.md
- Zheng et al. 2024: manuscripts/zheng2024.md
autodoc:
jupyter:
- in: bbconf/notebooks
out: bbconf/code
- in: geniml/notebooks
out: geniml/code