zamushwani

Qc Single Cell — Development skill for Claude Code

Development community

Quality control and filtering for single-cell RNA-seq.

How to install Qc Single Cell

Installs to ~/.claude/commands/zamushwani-biomedical-ai-skills-qc-single-cell.md

Terminal

mkdir -p ~/.claude/commands && curl -fsSL https://raw.githubusercontent.com/zamushwani/biomedical-ai-skills/HEAD/.claude/commands/qc-single-cell.md -o ~/.claude/commands/zamushwani-biomedical-ai-skills-qc-single-cell.md

Restart Claude Code, or start a new session, for it to be picked up.

What Qc Single Cell does

description: Quality control and filtering for single-cell RNA-seq. Use when the user has an h5ad/h5/10x matrix and wants QC, cell filtering, doublet detection, or asks why their cell count dropped. argument-hint: [h5ad-file] allowed-tools: Read Grep Glob Bash(python3 *)

Run QC on `$0`.

Follow the `single-cell-atlas` skill. The parts that are usually got wrong:

Use MAD-based thresholds, not fixed cutoffs. A hard n_genes > 200 throws away real cells in low-complexity tissue an

Alternatives in Development

Mempalace Search — Search your memories across the MemPalace using semantic search with wing/room filtering 58.6k ★
Vibe Kanban — Get 10X more out of Claude Code, Gemini CLI, Codex, Amp and other coding agents 23.5k ★
Diagnose Seq Scans — Remedy high seq scans on a table 7.2k ★