deconvolution-flashdeconv
CommunityUltra-fast spot deconvolution with FlashDeconv
Data & Analytics#deconvolution#spatial-transcriptomics#reference-based#adata#cell-type#flashdeconv#spot-level
Authorchenyhvvvv
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Fast and scalable deconvolution of spatial transcriptomics spots by using a reference-based method to estimate cell-type composition per spot.
Core Features & Use Cases
- Ultra-fast, reference-based deconvolution (FlashDeconv) with outputs stored in adata.obsm['flashdeconv'] and per-spot dominant cell type in adata.obs['celltype']
- Compatible with single-slice gene-expression data and a properly formatted scRNA-seq reference (.h5ad) with a celltype column
- No GPU needed; Python-based workflow designed for large spatial datasets
Quick Start
Run the FlashDeconv workflow on a spatial slice with a reference scRNA-seq dataset to obtain per-spot proportions and dominant cell types.
Dependency Matrix
Required Modules
scanpypandasnumpyflashdeconv
Components
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: deconvolution-flashdeconv Download link: https://github.com/chenyhvvvv/STAT-agent/archive/main.zip#deconvolution-flashdeconv Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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