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).
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: