openproblems-v2/src/joint_embedding/api/anndata_dataset.yaml at 1b2dd900cb0f13de52e5a038e0ee1adf354879cb · openproblems-bio/openproblems-v2 · GitHub

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type: file
description: "A raw dataset"
example: "dataset.h5ad"
info:
  label: "Dataset"
  slots:
    layers:
      - type: integer
        name: counts
        description: Raw counts
        required: true
    obs:
      - type: string
        name: batch
        description: Batch information
        required: true
      - type: double
        name: size_factors
        description: The size factors created by the normalisation method, if any.
        required: false
      - type: string
        name: cell_type
        description: Type of cells
        required: false
      - type: string
        name: pseudotime_order_GEX
        description:
        required: false
      - type: string
        name: pseudotime_order_ATAC
        description:
        required: false
      - type: string
        name: pseudotime_order_ADT
        description:
        required: false
      - type: double
        name: S_score
        description:
        required: false
      - type: double
        name: G2M_score
        description:
        required: false
      - type: boolean
        name: is_train
        description: if sample is train data
        required: true
    var:
      - type: string
        name: gene_ids
        description:
        required: false
      - type: string
        name: feature_types
        description:
        required: true
    uns:
      - type: string
        name: dataset_id
        description: "A unique identifier for the dataset"
        required: true
      - type: string
        name: organism
        description: "data from which organism "
        required: false
      - type: string
        name: gene_activity_var_names
        description:
        required: false
      - type: string
        name: sample_pm_varnames
        description:
        required: false