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yollct / spycone

Spicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data
GNU General Public License v3.0
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species object #4

Closed Tang-pro closed 1 month ago

Tang-pro commented 2 months ago

Hi, @yollct @kadam0 dset = spy.dataset(ts=data, transcript_id=transcriptid, gene_id = geneid, species=9606, keytype='entrezgeneid', timepts=4, reps1=3) Can I ask if I can use non-model species here, like cotton, because I see that the code has some parameters and species need to be provided

Tang-pro commented 1 month ago

Hi, @yollct @kadam0 Here my species is cotton, and the annotation information, which is not the NCBI version, is from the cotton website cottongen, here is how to solve it. Also I don't have BioNetwork, but I just want to cluster isoform-switch, does this affect

yollct commented 1 month ago

Hi,

No it doesn't affect if you just use the isoform-switch function. You can input any species in this case.

Best, Chit Tong