RNA-seq clustering of cell lines

I have data with rows that contain count data for each gene and columns that contain a specific cell line. I wish to perform a clustering analysis to determine which cell lines are most similar. I am unsure which tool is most useful for this as well as how to filter the data since some genes aren’t expressed (or only expressed in some of the cell lines).

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Hi @Coltin_Albitz

Find the Galaxy single-cell tutorials here for example tools/workflows:

If you are not sure where to start, the training event from last March has a suggested program, and single-cell analysis is covered with supplementary videos. The second video in the series is seems like a good match for where you are currently at with your own analysis.

Note: the Slack channel mentioned in this content is not active right now – so please use this forum or the GTN gitter chat instead for Q&A. FAQs: