Description

Export METASPACE datasets to AnnData and SpatialData objects

Input

Name
Description
Pattern

ds_id (string)

METASPACE dataset identifier to retrieve and convert to AnnData and SpatialData formats.

database_name_ (string)

Name of the metabolite annotation database to use (e.g., HMDB)

database_version_ (string)

Version of the annotation database to use (e.g., v4)

fdr_ (string)

False Discovery Rate threshold for filtering metabolite annotations.

^(0(\.[0-9]+)?|1(\.0+)?)$

use_tic_ (string)

Controls whether intensity values are scaled by the total ion count per pixel.

^(true|false)$

metadata_as_obs_ (string)

Whether to store metadata in the obs dataframe instead of uns.

^(true|false)$

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

Tools

metaspace_converter Documentation

Python package to download and convert datasets from the METASPACE knowledge base to common formats for single-cell and spatial omics analysis

https://github.com/metaspace2020/metaspace-converterLicense: Apache 2.0 license
Authors