Description

SCIMAP is a suite of tools that enables spatial single-cell analyses

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

cellByFeature (file)

CSV file with cell by feature table

*.{csv}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

annotedDataCsv (file)

Sorted CSV file

*.{csv}

annotedDataH5ad (file)

Sorted H5AD file

*.{h5ad}
included in
mcmicro
maintainer
Github user luiskuhn
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

scimap
MIT License

Scimap is a scalable toolkit for analyzing spatial molecular data.

scimap.xyz scimap.xyz/All%20Functions/A.%20Pre%20Processing/sm.pp.mcmicro_to_scimap https://github.com/labsyspharm/scimap