diff --git a/docs/geniml/changelog.md b/docs/geniml/changelog.md index 6acc545..ae8188c 100644 --- a/docs/geniml/changelog.md +++ b/docs/geniml/changelog.md @@ -2,6 +2,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. +## [0.2.0] -- 2024-02-20 + +- Fixed a bug with pydantic + ## [0.1.0] -- 2023-12-18 - First official released version of geniml diff --git a/mkdocs.yml b/mkdocs.yml index fbb4fcc..2a0cdae 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -82,24 +82,26 @@ nav: - Getting Started: - Module overviews: geniml/modules.md - How-to guides: - - Train region2vec embeddings: geniml/tutorials/region2vec.md - - Train single-cell embeddings: geniml/tutorials/train-scembed-model.md + - Cache BED files with BBClient: geniml/tutorials/bbclient.md - Tokenization: geniml/tutorials/tokenization.md - - Tokenize a BED file on the command line: geniml/tutorials/cli-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 - - Search intervals with BEDSpace: geniml/tutorials/bedspace.md - - Load vector database with embeddings: tutorials/load-qdrant-with-cell-embeddings.md - - Cell-type prediction using KNN: tutorials/cell-type-annotation-with-knn.md - Create consensus peaks: geniml/tutorials/create-consensus-peaks.md - Assess universe fit: geniml/tutorials/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 - - Tutorials: - - Using BEDspace: geniml/code/bedspace-analysis.md - Reference: - How to cite: citations.md - - API: geniml/autodoc_build/geniml.md + - API documentation: geniml/autodoc_build/geniml.md - Support: geniml/support.md - Contributing: geniml/contributing.md - Changelog: geniml/changelog.md