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anndata
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Extension repository on GitHub
Extension descriptor (YAML)

Read AnnData (.h5ad) files for single-cell genomics data analysis

Maintainer(s): honicky

Installing and Loading 

INSTALL anndata FROM community;
LOAD anndata;

Example 

-- Attach an AnnData file
ATTACH 'data.h5ad' AS scdata (TYPE ANNDATA);

-- Query cell metadata
SELECT * FROM scdata.obs LIMIT 10;

-- Query gene metadata
SELECT * FROM scdata.var LIMIT 10;

-- Query expression matrix
SELECT * FROM scdata.X LIMIT 10;

-- Detach when done
DETACH scdata;

About anndata

The AnnData extension provides read-only access to AnnData (.h5ad) files, the standard format for single-cell genomics data.

ATTACH Syntax 

ATTACH 'file.h5ad' AS name (TYPE ANNDATA);

Available Tables

  • obs - Observation (cell) metadata
  • var - Variable (gene) metadata
  • X - Expression matrix (genes as columns)
  • obsm_* - Dimensional reductions (PCA, UMAP, etc.)
  • varm_* - Variable embeddings
  • layers_* - Alternative expression matrices
  • obsp_* - Cell-cell pairwise matrices
  • varp_* - Gene-gene pairwise matrices
  • uns - Unstructured metadata

Table Functions 

-- Core data
SELECT * FROM anndata_scan_obs('file.h5ad');
SELECT * FROM anndata_scan_var('file.h5ad');
SELECT * FROM anndata_scan_x('file.h5ad');

-- Dimensional reductions
SELECT * FROM anndata_scan_obsm('file.h5ad', 'X_pca');
SELECT * FROM anndata_scan_obsm('file.h5ad', 'X_umap');

-- Layers
SELECT * FROM anndata_scan_layers('file.h5ad', 'raw');

-- File info
SELECT * FROM anndata_info('file.h5ad');

Added Functions

function_name function_type description comment examples
anndata_hello scalar NULL NULL  
anndata_info table NULL NULL  
anndata_scan_layers table NULL NULL  
anndata_scan_obs table NULL NULL  
anndata_scan_obsm table NULL NULL  
anndata_scan_obsp table NULL NULL  
anndata_scan_uns table NULL NULL  
anndata_scan_var table NULL NULL  
anndata_scan_varm table NULL NULL  
anndata_scan_varp table NULL NULL  
anndata_scan_x table NULL NULL  
anndata_version scalar NULL NULL