AN
Data & Repro
AnnData
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Data & Repro
BI
bio-single-cell-data-io
Maintainer FreedomIntelligence · Last updated April 1, 2026
Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating Seurat objects and AnnData objects, and converting between formats. Use when loading, saving, or converting single-cell data formats.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-single-cell-data-io
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Read, write, and create single-cell data objects for analysis.
- adata = sc.read_10x_mtx('filtered_feature_bc_matrix/', var_names='gene_symbols', cache=True) print(f'Loaded {adata.n_obs} cells x {adata.n_vars} genes').
Source Doc
Excerpt From SKILL.md
Scanpy (Python)
Goal: Load, create, and save single-cell data objects using Scanpy and AnnData.
Approach: Read 10X Genomics output, CSV, or Loom formats into AnnData objects, manipulate metadata and layers, and write to h5ad format.
"Load my 10X data" → Read Cell Ranger output directory or h5 file into an AnnData object with expression matrix, cell barcodes, and gene annotations.
Read 10X h5 file directly
adata = sc.read_10x_h5('filtered_feature_bc_matrix.h5')
## - adata.layers: alternative matrices (raw counts, normalized)
print(f'Shape: {adata.shape}')
print(f'Cell metadata: {adata.obs.columns.tolist()}')
print(f'Gene metadata: {adata.var.columns.tolist()}')
Use cases
- Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating Seurat objects and AnnData objects, and converting between formats.
- Use when loading, saving, or converting single-cell data formats.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- preprocessing - QC filtering and normalization after loading
- clustering - Dimensionality reduction and clustering
- markers-annotation - Find marker genes and annotate cell types
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