Overall

New: A command-line version of SOView is available at SOView

This repo contains code related to SODB and its companion command-line package pysodb.

• Data Processing
• Figure Regeneration
• Benchmarking
• Demonstration

SODB overview

Key resources

Category	Purpose	Figure	Code
Website	Website of SODB	None	Link
Website	Website of pysodb	None	Link
Data Processing	Process Raw data to Anndata format	None	Link
Data Processing	Process Anndata format to SODB ready	None	Link
Figure Regeneration	Compare with related works	Fig. 1g	Link
Figure Regeneration	Timeline plot of spatial omics	Fig. 2a	Link
Figure Regeneration	Pie chart of category statistics of datasets	Fig. 2bcdgh	Link
Figure Regeneration	Tree plot of human and mouse studies	Fig. 2ef	Link
Figure Regeneration	Boxplot of SE features and data sparsity	Fig. 2ij	Link
Figure Regeneration	Other figures	Fig. 3~5	Generated by SODB website
Figure Regeneration	Computational methods covered by review papers	Fig. 6a	Link
Figure Regeneration	Methods supported by SODB	Fig. 6bcd	Link
Figure Regeneration	Datasets frequency analysis	Fig. 6ef	Link
Figure Regeneration	4i spatial proteomics analysis	Fig. S14	Link
Figure Regeneration	Country distribution	Fig. S6	Link
Benchmarking	Benchmark analysis of data loading	Fig. S24	Link
Benchmarking	Benchmark analysis of spatial domain	Fig. S25~42	Link
Demonstration	Tutorial of pysodb	None	Link
Demonstration	Demonstrate the compatibility with SCANPY and Squidpy	Fig. 1	Link

Cite

Yuan, Z., Pan, W., Zhao, X. et al. SODB facilitates comprehensive exploration of spatial omics data. Nat Methods (2023). https://doi.org/10.1038/s41592-023-01773-7
Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data. Nat Methods (2023). https://doi.org/10.1038/s41592-023-01772-8