sc-adaptive-qc
CommunityAdaptive QC for scRNA-seq with doublet removal.
Data & Analytics#scanpy#scrublet#doublet-detection#sc_rna_seq#adaptive-qc#mitochondrial-filtering#min-genes-filter
Authorya-way
Version1.0.0
Installs0
System Documentation
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.
Dependency Matrix
Required Modules
scanpynumpyscrublet
Components
scripts
💻 Claude Code Installation
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Please help me install this Skill: Name: sc-adaptive-qc Download link: https://github.com/ya-way/cytoclaw-skills/archive/main.zip#sc-adaptive-qc Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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