sc-adaptive-qc

Filter scRNA-seq cells by mito and gene thresholds and remove doublets.

Updated Mar 30, 2026

Search Tags:#scanpy #scrublet #doublet-detection #sc_rna_seq #adaptive-qc #mitochondrial-filtering #min-genes-filter

Ready to run

npx skills add https://github.com/ya-way/cytoclaw-skills --skill sc-adaptive-qc

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: sc-adaptive-qc
Source: https://github.com/ya-way/cytoclaw-skills/tree/main/workspace/skills/sc-adaptive-qc
Command: npx skills add https://github.com/ya-way/cytoclaw-skills --skill sc-adaptive-qc

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires scanpy, numpy, scrublet, and includes scripts (resource) components.

What problem does it solve?

Adaptive single-cell QC filtering with user-specified mitochondrial and gene thresholds, followed by doublet removal and saving qc_filtered.h5ad.

Core Features & Use Cases

Threshold-based QC using max mito percent and min genes per cell
Optional Scrublet-based doublet detection with safe fallback
Outputs include qc_filtered.h5ad and adaptive_qc_summary.json

Quick Start

Run the script with your input path, maximum mitochondrial percent, minimum genes per cell, and an output directory to create qc_filtered.h5ad and a summary.

Frequently Asked Questions about sc-adaptive-qc

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I perform scRNA-seq QC filtering and doublet removal on 10x data?▼

scRNA-seq QC filtering applies user-specified mitochondrial percentage and minimum gene thresholds to raw 10x data, followed by doublet removal to produce a cleaned h5ad file. It reports cell counts before and after filtering.

Does Scanpy work with Scrublet for doublet detection in single-cell RNA-seq?▼

Scanpy works with Scrublet for optional doublet detection in single-cell RNA-seq data. If Scrublet is unavailable, the Skill uses a safe fallback heuristic to continue removing doublets.

What thresholds do I need to set for adaptive single-cell RNA-seq quality control?▼

Adaptive single-cell RNA-seq quality control requires setting a maximum mitochondrial percentage and a minimum number of genes per cell. These thresholds filter out low-quality cells before doublet removal.

What is the best way to remove doublets from raw 10x scRNA-seq data?▼

The best way to remove doublets from raw 10x scRNA-seq data is using threshold-based QC combined with Scrublet detection. This process outputs a qc_filtered.h5ad file and a summary JSON with the doublet rate.

Why does scRNA-seq quality control report cell counts before and after filtering?▼

scRNA-seq quality control reports cell counts before and after filtering to track data loss from mitochondrial and gene thresholding, plus doublet removal. It outputs this tracking information in an adaptive_qc_summary.json file.

Can I use this adaptive QC method if Scrublet fails during doublet detection?▼

You can still run adaptive QC if Scrublet fails because the process includes a safe fallback heuristic for doublet detection. This ensures your scRNA-seq data still gets cleaned and exported as qc_filtered.h5ad.