Tutorials

In general, you need to make three objects (Train, TopModel and Analysis).

The Train object can be initialized either from (a) single cell RNA-seq dataset or (b) single cell ATAC-seq or (c) bulk RNA-seq.

Training part can be time-consuming depending on how big your data is, however you can learn each train model per random state in different jobs and then combine all together. Look at this tutorial for mor information.

For guidance on using Topyfic to analyze your data look at our more depth-in tutorials:

• Analysing single cell C2C12 data only using regulatory elements: Analysing single cell and single nucleus using C2C12 ENCODE datasets using regulatory elements instead of all genes.

• Analysing single cell microglia data: Analysing single cell microglia data from Model-AD portal.