Table 1 Software and algorithms used in data analysis

From: Single cell spatial analysis reveals inflammatory foci of immature neutrophil and CD8 T cells in COVID-19 lungs

Name of software

Source

Identifier

imctools

https://github.com/BodenmillerGroup/imctools

RRID:SCR_017132

Deepcell

https://vanvalen.github.io/about/

RRID:SCR_022197

Phenograph

https://github.com/JinmiaoChenLab/Rphenograph

RRID:SCR_016919

Harmony

https://github.com/slowkow/harmonypy

RRID:SCR_022206

Slingshot

https://github.com/kstreet13/slingshot

RRID:SCR_017012

Ruffus

http://www.ruffus.org.uk/

RRID:SCR_022196

QuPath

https://qupath.github.io/

https://doi.org/10.1038/s41598-017-17204-5

MCD

https://www.standardbio.com/products-services/software

RRID:SCR_023007

Catalyst R

http://bioconductor.org/packages/CATALYST/

RRID:SCR_017127

Harmony

https://github.com/immunogenomics/harmony

RRID:SCR_022206

diffcyt R package (version 1.8.8)

https://www.bioconductor.org/packages/release/bioc/html/diffcyt.html

RRID:SCR_023006

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