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anndata - Single-cell annotated data structure

Python package for handling annotated data matrices with efficient storage and manipulation

Tags

Updated: 2026-06-30
data structuresingle-cellgenomicsbioinformaticsmatrixh5adscverse

Capabilities

create AnnData objectsread h5ad fileswrite h5ad filesread CSV files

Typical Inputs

h5ad filesCSV filesZarr files

Typical Outputs

h5ad filesZarr filesCSV files

What this skill does

  • create AnnData objects
  • read h5ad files
  • write h5ad files
  • read CSV files
  • read Zarr files
  • write Zarr files
  • read Loom files
  • read 10X files
  • subset data
  • filter data
  • transform data
  • concatenate datasets
  • add metadata

Inputs

  • h5ad files
  • CSV files
  • Zarr files
  • Loom files
  • 10X H5 files
  • MTX files
  • Excel files
  • NumPy arrays
  • Pandas DataFrames
  • sparse matrices

Outputs

  • h5ad files
  • Zarr files
  • CSV files
  • AnnData objects
  • data subsets
  • concatenated datasets

Requirements

  • Python environment
  • uv package manager

Source

  • Spec: SKILL.md

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