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
      • 3.1.1. 10X Matrix format
      • 3.1.2. Scanpy object
      • 3.1.3. Seurat object
      • 3.1.4. Tile DB format
      • 3.1.5. Full matrix dataframe
    • 3.2. Option 2: Submit study from local machine
      • 3.2.1. 10X Matrix format
      • 3.2.2. Scanpy object
      • 3.2.3. Seurat object
      • 3.2.4. Full matrix dataframe
    • 3.3. Option 3: Submit study with shared s3 of a group
      • 3.3.1. 10X Matrix format
      • 3.3.2. Scanpy object
      • 3.3.3. Seurat object
      • 3.3.4. Tile DB format
      • 3.3.5. Full matrix dataframe
  • 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
      • 5.4.1. List all embeddings
      • 5.4.2. Access an embedding
    • 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
      • 3.1.1. Visium format
      • 3.1.2. DSP format
      • 3.1.3. Visium Scanpy object
      • 3.1.4. Visium Seurat object
    • 3.2. Option 2: Submit study from local machine
      • 3.2.1. Visium format
      • 3.2.2. DSP format
      • 3.2.3. Visium Scanpy object
      • 3.2.4. Visium Seurat object
    • 3.3. Option 3: Submit study with shared s3 of a group
      • 3.1.1. Visium format
      • 3.1.2. DSP format
      • 3.1.3. Visium Scanpy object
      • 3.1.4. Visium Seurat object
  • 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
      • 5.4.1. List all embeddings
      • 5.4.2. Access an embedding
    • 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, …)
      • 3.1.1. Option 1: Submit study from s3
      • 3.1.2. Option 2: Submit study from local machine / server
      • 3.1.3. Option 3: Submit study with shared s3 of a group
    • 3.2. Submit proteomics dataset (CODEX, AKOYA, …)
      • 3.2.1. Option 1: Submit study from s3
      • 3.1.2. Option 2: Submit study from local machine / server
      • 3.2.3. 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
      • 5.4.1. List all embeddings
      • 5.4.2. Access an embedding
    • 5.5. Query genes
  • 6. Standardize your metadata
    • 6.1. Retrieve ontology tree
    • 6.2. Assign standardized terms