search

petitmingchang / TO-GCN_STAR-Protocol

TO-GCN tools for STAR-Protocol
5 stars 0 forks source link

Whether TOGCN can be implemented in large-scale samples to build a dynamic regulatory network #2

Open mingjiayuan opened 7 months ago

mingjiayuan commented 7 months ago

Dear author, Hello, now I have dozens of time transcriptome data of a plant tissue for several months. Can we implement TOGCN in these samples and build a dynamic regulatory network? If so, how can we select seed genes? I'd appreciate it if you could answer it

petitmingchang commented 7 months ago

@mingjiayuan Generally speaking, we want to use one or more genes whose expression pattern are highly expressed at first time point and lowly expressed at all following time points. To identify these genes you can use the "MFselector" R package describe in the same STAR Protocol or simply use clustering to get genes that shows the expression pattern.

Shaimaa264 commented 7 months ago

mfselector

How can I download the MFSelector package when the download link is not working in browser or R studio?

petitmingchang commented 7 months ago

@Shaimaa264 Thank you for reporting the issue. We will check it and get back to you soon.

petitmingchang commented 7 months ago

@Shaimaa264 Please use the links (listed in the STAR protocol) below to download the MFselector R package: http://microarray.bmi.nycu.edu.tw:8080/tools/module/MFSelector/index.jsp?mode=home or http://microarray.bmi.nycu.edu.tw:8080/tools/module/MFSelector/content/support/multicore/MFSelector_1.0.tar.gz