nf-core/metaspace_converter

module

Export METASPACE datasets to AnnData and SpatialData objects

anndata spatialdata metabolomics mass spectrometry imaging

Module Information

Repository: https://github.com/nf-core/modules/tree/master/modules/nf-core/metaspace/converter
Source: nf-core
Organization: nf-core
Authors: @bisho2122
Maintainers: @bisho2122

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

License: Apache 2.0 license

Name	Type	Description
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.
use_tic_	string	Controls whether intensity values are scaled by the total ion count per pixel.
metadata_as_obs_	string	Whether to store metadata in the obs dataframe instead of uns.

Include this module in your Nextflow pipeline:

include { METASPACE_CONVERTER } from 'https://github.com/nf-core/modules/tree/master/modules/nf-core/metaspace/converter'