bio-single-cell-data-io
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-data-io --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Cell Ranger 8.0+, anndata 0.10+, numpy 1.26+, pandas 2.2+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Single-Cell Data I/O Read, write, and create single-cell data objects for analysis. ## 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. ### Required Imports ```python import scanpy as sc import anndata as ad import pandas as pd import numpy as np ``` ### Reading 10X Genomics Data ```python # Read 10X cellranger output (filtered
- Version Compatibility
- Scanpy (Python)
- Required Imports
- Reading 10X Genomics Data
- AnnData Object Structure
- Creating AnnData from Matrix
- Reading/Writing h5ad Files
- Reading Other Formats
- Adding Metadata
- Subsetting AnnData
- Storing Raw Counts
- Seurat (R)
- Required Libraries
- Reading 10X h5 File
What does the bio-single-cell-data-io skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-single-cell-data-io --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.