You just need to supply this along with your pathways that you want to analyse. SCPA can be applied directly on Seurat and SCE objects, as well as manually subsetted expression matrices. It will install the latest Composer version and set up your PATH so that you can call composer from any directory in your command line. This means you can assess pathway activity through multiple stimulation phases, or across cell differentiation SCPA allows for multisample testing, so you can compare multiple conditions simultaneously e.g. compare across 3 time points, or across multiple phases of a pseuodotime trajectory. For more on this, see our SCPA interpretation page You essentially get the best of both worlds, as pathways with changes in multivariate distribution (high qval) but no overall enrichment (low fold change) are still interestingly different pathways, as we show in our paper. Multivariate distribution testing allows for the identification of pathways that show enrichment in a given population AND also pathways that show transcriptional change independent of enrichment. This approach allows for a number of benefits over current methods: It’s a different approach to pathway analysis that defines pathway activity as a change in multivariate distribution of a given pathway across conditions, rather than enrichment or over representation of genes. SCPA is a method for pathway analysis in single cell RNA-seq data.
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