Deutsch

anndata

Downloads

654

GitHub-Sterne

9

Erweiterungs-Repository auf GitHub

Lesen von AnnData-Dateien (.h5ad) für die Analyse von Single-Cell-Genomikdaten, mit Unterstützung für lokale und entfernte Dateien (HTTP/HTTPS/S3)

Maintainer: honicky

Installation und Laden

INSTALL anndata FROM community;
LOAD anndata;

Beispiel

-- 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;

Über anndata

Die AnnData-Erweiterung bietet schreibgeschützten Zugriff auf AnnData-Dateien (.h5ad), das Standardformat für Single-Cell-Genomikdaten.

ATTACH-Syntax

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


-- Remote file via HTTPS
ATTACH 'https://example.com/data.h5ad' AS name (TYPE ANNDATA);


-- S3 file (requires httpfs extension and credentials)
INSTALL httpfs;
LOAD httpfs;
CREATE SECRET s3_secret (TYPE S3, KEY_ID 'xxx', SECRET 'xxx', REGION 'us-east-1');
ATTACH 's3://bucket/data.h5ad' AS name (TYPE ANNDATA);


-- With custom gene name/ID columns
ATTACH 'file.h5ad' AS name (TYPE ANNDATA, VAR_NAME_COLUMN 'gene_symbols', VAR_ID_COLUMN 'ensembl_id');

Verfügbare Tabellen

  • obs - Beobachtungsmetadaten (Zellen)
  • var - Variablenmetadaten (Gene)
  • X - Expressionsmatrix (Gene als Spalten)
  • obsm_* - Dimensionsreduktionen (PCA, UMAP usw.)
  • varm_* - Variablen-Embeddings
  • layers_* - Alternative Expressionsmatrizen
  • obsp_* - paarweise Zell-Zell-Matrizen
  • varp_* - paarweise Gen-Gen-Matrizen
  • uns - unstrukturierte Metadaten

Tabellenfunktionen

-- 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');

Mehrdatei-Abfragen mit Wildcards

Alle Scan-Funktionen unterstützen Glob-Muster, um über mehrere Dateien hinweg abzufragen. Eine Spalte _file_name wird automatisch hinzugefügt, um die Quelldatei zu kennzeichnen.

-- Query obs metadata across all .h5ad files in a directory
SELECT * FROM anndata_scan_obs('samples/*.h5ad');


-- Intersection mode (default): only columns shared by all files
SELECT * FROM anndata_scan_obs('samples/*.h5ad', schema_mode := 'intersection');


-- Union mode: all columns, NULL where a file lacks a column
SELECT * FROM anndata_scan_obs('samples/*.h5ad', schema_mode := 'union');


-- Expression data across files (intersection of genes by default)
SELECT * FROM anndata_scan_x('samples/*.h5ad');


-- Union of genes across files
SELECT * FROM anndata_scan_x('samples/*.h5ad', schema_mode := 'union');


-- Works with S3 paths
SELECT * FROM anndata_scan_obs('s3://bucket/project/*.h5ad');


-- Multiple patterns
SELECT * FROM anndata_scan_obs(['batch_a/*.h5ad', 'batch_b/*.h5ad']);

Hinzugefügte Funktionen

function_name function_type description comment examples
anndata_info table Returns metadata and structure information about an AnnData (.h5ad) file, including the number of observations, variables, available layers, embeddings, and other components. NULL [SELECT * FROM anndata_info(‘data.h5ad’);]
anndata_scan_obs table Scans the observation (cell) metadata from an AnnData file. Returns all columns from the obs DataFrame including cell barcodes, cell types, and other annotations. NULL [SELECT * FROM anndata_scan_obs(‘data.h5ad’) LIMIT 5;]
anndata_scan_var table Scans the variable (gene) metadata from an AnnData file. Returns all columns from the var DataFrame including gene IDs, gene names, and other annotations. NULL [SELECT * FROM anndata_scan_var(‘data.h5ad’) LIMIT 5;]
anndata_scan_x table Scans the main expression matrix (X) from an AnnData file. Returns the matrix with observation indices as rows and gene names as columns. Automatically handles both dense and sparse matrix formats. NULL [SELECT obs_idx, CD3D, CD19, CD14 FROM anndata_scan_x(‘data.h5ad’) LIMIT 5;]
anndata_scan_obsm table Scans observation embeddings (obsm) from an AnnData file. Common embeddings include PCA (X_pca), UMAP (X_umap), and t-SNE (X_tsne). NULL [SELECT * FROM anndata_scan_obsm(‘data.h5ad’, ‘X_umap’) LIMIT 5;]
anndata_scan_varm table Scans variable embeddings (varm) from an AnnData file. These are gene-level embeddings such as PCA loadings. NULL [SELECT * FROM anndata_scan_varm(‘data.h5ad’, ‘PCs’) LIMIT 5;]
anndata_scan_layers table Scans alternative expression matrices (layers) from an AnnData file. Common layers include raw counts, normalized data, or scaled data. NULL [SELECT * FROM anndata_scan_layers(‘data.h5ad’, ‘raw’) LIMIT 5;]
anndata_scan_obsp table Scans observation pairwise matrices (obsp) from an AnnData file. These typically contain cell-cell distance or connectivity matrices. NULL [SELECT * FROM anndata_scan_obsp(‘data.h5ad’, ‘distances’) LIMIT 5;]
anndata_scan_varp table Scans variable pairwise matrices (varp) from an AnnData file. These contain gene-gene relationship matrices. NULL [SELECT * FROM anndata_scan_varp(‘data.h5ad’, ‘correlations’) LIMIT 5;]
anndata_hello scalar NULL NULL NULL
anndata_version scalar NULL NULL NULL
anndata_scan_raw_var table NULL NULL NULL
anndata_scan_raw_varm table NULL NULL NULL
anndata_scan_raw_x table NULL NULL NULL
anndata_scan_uns table NULL NULL NULL

Überladene Funktionen

Diese Erweiterung fügt keine Funktionsüberladungen hinzu.

Hinzugefügte Typen

Diese Erweiterung fügt keine Typen hinzu.

Hinzugefügte Einstellungen

Diese Erweiterung fügt keine Einstellungen hinzu.