your_file.txt

single-cell-python-packages:
  description: Vector database of single-cell python packages.
  type: vector_db
  parameters:
    embedding_model: text-embedding-3-large
    chunk_size: 4000
    chunk_overlap: 200
  items:
    scanpy:
      type: package documentation
      url: https://scanpy.readthedocs.io/en/stable/index.html
    anndata:
      type: package documentation
      url: https://anndata.readthedocs.io/en/latest/
    scvi-tools:
      type: package documentation
      url: https://docs.scvi-tools.org/en/stable/
    squidpy:
      type: package documentation
      url: https://squidpy.readthedocs.io/en/stable/
    dynamo:
      type: package documentation
      url: https://dynamo-release.readthedocs.io/en/latest/
    CellphoneDB:
      type: package documentation
      url: https://cellphonedb.readthedocs.io/en/latest/
    omicverse:
      type: package documentation
      url: https://starlitnightly.github.io/omicverse/
    spateo:
      type: package documentation
      url: https://spateo-release.readthedocs.io/en/latest/
    spatialdata:
      type: package documentation
      url: https://spatialdata.scverse.org/en/latest/
    muon:
      type: package documentation
      url: https://muon.readthedocs.io/en/latest/
    mudata:
      type: package documentation
      url: https://mudata.readthedocs.io/en/latest/
    scirpy:
      type: package documentation
      url: https://scirpy.scverse.org/en/latest/
    scvelo:
      type: package documentation
      url: https://scvelo.readthedocs.io/en/stable/
    pydeseq2:
      type: package documentation
      url: https://pydeseq2.readthedocs.io/en/latest/
    CellOracle:
      type: package documentation
      url: https://morris-lab.github.io/CellOracle.documentation/
    Moscot:
      type: package documentation
      url: https://moscot.readthedocs.io/en/latest/
    liana:
      type: package documentation
      url: https://liana-py.readthedocs.io/en/latest/
    sopa:
      type: package documentation
      url: https://gustaveroussy.github.io/sopa/
    tangram:
      type: package documentation
      url: https://tangram-sc.readthedocs.io/en/latest/index.html
    cellxgene-census:
      type: package documentation
      url: https://chanzuckerberg.github.io/cellxgene-census/index.html
    cellrank:
      type: package documentation
      url: https://cellrank.readthedocs.io/en/latest/
    bento-tools:
      type: package documentation
      url: https://bento-tools.readthedocs.io/en/latest/index.html
    hotspotsc:
      type: package documentation
      url: https://hotspot.readthedocs.io/en/latest/index.html
    Palantir:
      type: package documentation
      url: https://palantir.readthedocs.io/en/latest/
    pertpy:
      type: package documentation
      url: https://pertpy.readthedocs.io/en/latest/
    cell2location:
      type: package documentation
      url: https://pertpy.readthedocs.io/en/stable/
    snapatac2:
      type: package documentation
      url: https://kzhang.org/SnapATAC2/index.html