Issues differential expression about swan_vis HOT 3 CLOSED

So I tried out the DE module on a SwanGraph I have lying around and I get positive and negative log2fc values, so I am not sure what's going on there either :( If you send me your SwanGraph I can possibly take a look.

With regards to the low read count test, that is definitely a good idea. I will add a read count threshold for these tests to my to-do list for the next release.

As an aside, the DE testing library that Swan uses (diffxpy), is not really actively supported so I unfortunately recommend using a more robust, better supported tool such as edgeR or DEseq2 to perform differential expression testing in your data. If you want I can point you to some code examples that I have used to run such tests on my long read data.

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As an aside, the DE testing library that Swan uses (diffxpy), is not really actively supported

This is changing and the lab is currently overhauling the backend :)

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This is changing and the lab is currently overhauling the backend :)

Wow this is really great to hear! I eagerly await the update; there is such a disappointing lack of DE tools in Python.

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