Find dynamics genes in branches

[jphe]

Hi,

I have used harmony for my data, it works quite well, very great tools. But I have another question which may outside the scope of current harmony. I have already found the different branches for my data, but I want to know why it has those branches, so we want to check what is the dynamics expressed genes in one branch, and what is the different expressed genes between different branches. Dose harmony has any function to do this, or do you have any suggestions how can I do this with other tools. Very appreciate for your help.

Best regards,
Jphe

[ManuSetty]

Glad that Harmony was helpful in your research! We don't have a method built into Harmony for differential expression, but the EMD technique highlighted in the MAGIC paper can be used to identify differentially expressed genes post imputation. A Matlab script developed by @roshan9128 is attached for this purpose.

If you are interested in identify genes that show similar dynamics in one or more branches, you can also use Phenograph to cluster the expression trends themselves. See example in Palantir notebook here.

Finally, we have observed that

[jphe]

Glad that Harmony was helpful in your research! We don't have a method built into Harmony for differential expression, but the EMD technique highlighted in the MAGIC paper can be used to identify differentially expressed genes post imputation. A Matlab script developed by @roshan9128 is attached for this purpose.

If you are interested in identify genes that show similar dynamics in one or more branches, you can also use Phenograph to cluster the expression trends themselves. See example in Palantir notebook here.

Finally, we have observed that

Thanks for your suggestions, I'm tying Palantir, but it seems dose not compatible with the latest version of rpy2, it only works for the 2.9.5 and lower version of rpy2.

[ManuSetty]

Thanks for the tip. I will update the requirements and then fix the issue at a later time.