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how to read graph_test output of monocle 3 #716

Open synatkeamsk opened 2 months ago

synatkeamsk commented 2 months ago

Dear All,

I am using monocle 3 to perform Trajectory analysis and use deg <- graph_test(cds, neighbor_graph = "principal_graph") to examine genes that changed as a function of pseudotime. I am a bit unfamiliar with the output and have read the monocle3 documentation, but still unclear.

The output I got contain various columns such as gene names, status, p_value, morans_test_statistics, morans_I and q_value. I am wondering how do I know which genes are downregulated or upregulated based on these columns? I have attached the image of the output I got. Hope someone can help. Thanks in advance!

Best,

Capture

synatkeamsk commented 4 weeks ago

Dear developers, @ctrapnell @kou @dcalderon @Loyale !

Hope you are well. I am wondering whether anyone of you could help answer my questions above. Recently, I have also try TradeSeq to find DEG from monocle3 object. What do you think about tradeseq. Hope you could spare a couple of minutes help because I am still stuck with it.

Kind Regards,

Synat