Examples

API

• Axis Query Example
  • Opening the Census
  • Summarize Census cell metadata
  • Full census stats
• Computing on X: using online algorithms
  • Simple incremental (aka “online”) calculations
  • Complex online calculations
  • A more complex example - counting cells per feature, grouped by dataset_id
• Census datasets presence
  • Is a feature present in a dataset?
  • What datasets contain a feature?
  • What features are in a dataset?
• Census Datasets example
• Census query & extract subsets
• Census - demo ScanPy rank_gene_groups
• Census summary cell counts example

Analysis

• Learning about the CELLxGENE Census
  • Contents
  • Opening the Census
  • Census organization
  • Census summary content tables
  • Cell metadata
  • Gene metadata
  • Understanding Census contents beyond the summary tables
• Integration of data from the Census
  • Finding and fetching data from mouse liver
  • Gene-length normalization of Smart-Seq2 data.
  • Integration with scvi-tools
• Exploring all data from a tissue in the Census
  • Learning about the lung data in the Census
  • Fetching a sample of all human lung data from the Census.
• Normalizing full-length gene sequencing data from the Census
  • Contents
  • Opening the census
  • Fetching full-length example sequencing data (Smart-Seq)
  • Normalizing expression to account for gene length
  • Validation through clustering analysis
• Querying and fetching data from the Census
  • Contents
  • Opening the census
  • Querying cell metadata (obs)
  • Querying gene metadata (var)
  • Querying expression data