Welcome to bioturing_connector’s documentation!

Contents:

• Installation
• API
  • Constants
    • bioturing_connector.typing package
      • Module contents
  • bioturing_connector package
    • bioturing_connector.bbrowserx_connector module
      • BBrowserXConnector
    • bioturing_connector.lens_bulk_connector module
      • LensBulkConnector
    • bioturing_connector.lens_sc_connector module
      • LensSCConnector
• Tutorial
  • SDK_Document_BBrowserX
    • Installation
    • 1. Connect to host server
    • 2. List groups, studies and s3
      • 2.1. Get info of available groups
      • 2.2. List all available studies in a group
      • 2.3. List all s3 bucket of current user
      • 2.4. List all shared s3 of a group
    • 3. Submit study
      • 3.1. Option 1: Submit study from s3
      • 3.2. Option 2: Submit study from local machine
      • 3.3. Option 3: Submit study with shared s3 of a group
    • 4. Submit metadata
      • 4.1. Submit a dataframe directly
      • 4.2. Submit file from local / server
      • 4.3. Submit file from s3
      • 4.4. Submit file from shared s3 of a group
    • 5. Access study data
      • 5.1. Get barcodes
      • 5.2. Get features
      • 5.3. Get metadata dataframe
      • 5.4. Get embeddings
      • 5.5. Query genes
    • 6. Standardize your metadata
      • 6.1. Retrieve ontology tree
      • 6.2. Assign standardized terms
  • SDK_Document_Lens_Bulk
    • Installation
    • 1. Connect to host server:
    • 2. List groups, studies and s3
      • 2.1. Get info of available groups
      • 2.2. List all available studies in a group
      • 2.3. List all s3 bucket of current user
      • 2.4. List all shared s3 of a group
    • 3. Submit study
      • 3.1. Option 1: Submit study from s3
      • 3.2. Option 2: Submit study from local machine
      • 3.3. Option 3: Submit study with shared s3 of a group
    • 4. Submit metadata
      • 4.1. Submit a dataframe directly
      • 4.2. Submit file from local / server
      • 4.3. Submit file from s3
      • 4.4. Submit file from shared s3 of a group
    • 5. Access study data
      • 5.1. Get barcodes
      • 5.2. Get features
      • 5.3. Get metadata dataframe
      • 5.4. Get embeddings
      • 5.5. Query genes
    • 6. Standardize your metadata
      • 6.1. Retrieve ontology tree
      • 6.2. Assign standardized terms
  • SDK_Document_Lens_SC
    • Installation
    • 1. Connect to host server
    • 2. List groups, studies and s3
      • 2.1. Get info of available groups
      • 2.2. List all available studies in a group
      • 2.3. List all s3 bucket of current user
      • 2.4. List all shared s3 of a group
    • 3. Submit study
      • 3.1. Submit single cell - spatial dataset (COSMX, VISIUM, VIZGEN, …)
      • 3.2. Submit proteomics dataset (CODEX, AKOYA, …)
    • 4. Submit metadata
      • 4.1. Submit a dataframe directly
      • 4.2. Submit file from local / server
      • 4.3. Submit file from s3
      • 4.4. Submit file from shared s3 of a group
    • 5. Access study data
      • 5.1. Get barcodes
      • 5.2. Get features
      • 5.3. Get metadata dataframe
      • 5.4. Get embeddings
      • 5.5. Query genes
    • 6. Standardize your metadata
      • 6.1. Retrieve ontology tree
      • 6.2. Assign standardized terms