The CoxMX SMI platform is one of several new and upcoming technologies for measuring spatially-resolved gene expression at the single cell level. New technologies invariably mean new analytical challenges, and new analytical toolkits. So spatially resolved single cell RNAseq toolkits will continue to evolve rapidly; but what are our current options?
Ahead of the arrival of a CosMx SMI platform - and the subsequent wave of data it will produce, this work explores a public lung cancer CosMX dataset using established and familiar analysis tools. The suitability of tools is evaluated from a ‘core’ bioinformatics perspective - on the basis ease of use, documentation, interoperability and computational requirements. The goal of this work is to identify a practical starting suite of reliable and generically useful tools that form a platform for downstream biological analyses.