You teach everything in the easiest way. Because of you it has been possible to understand clusteting , layout , directed - undirected networks and more. Thanks a lot . Could you please explain the nested network and cytoscape automation ?
Thanks a lot! Regarding nested networks, they are quite easy to make: if you have a session with multiple networks, you can simple right-click a node in one network and choose another network to be put on that network (i.e. be nested). That allows you to make a network of networks, but I cannot think of a situation where I would want to do that, which makes it hard to make a compelling video about. Cytoscape automation is very useful, as it allows you to effectively "remote control" Cytoscape from a script, which can be great for making analyses reproducible. The problem from a video perspective is that it effectively becomes a programming video.
I believe the only option at the moment is to do a screenshot. However, that is not as bad as it sounds. To get a "clean" image, you can get a white background by choosing the "Light" color scheme and turn off the coordinate system under Scene Actions. Given the resolution of modern monitors, you should get an image that is more than 300 dpi when printed the size of a figure in a journal. I wish it was possible to export as vector graphics, but I suspect it would be a lot of work to implement.
You teach everything in the easiest way. Because of you it has been possible to understand clusteting , layout , directed - undirected networks and more. Thanks a lot . Could you please explain the nested network and cytoscape automation ?
I cannot think of an elegant way to do this in just Cytoscape. Unless you first do some scripting to filter the miRNA network, you would have to import the entire network into Cytoscape. The latter is possible, but it would be very slow.
Dear Jensen thank you for the videos they are great explained. Kindly can I get your email. I need your help with some big data of protein concerns my study and I want to use Gene set enrichment analysis to classify them. Thank you.
You teach everything in the easiest way. Because of you it has been possible to understand clusteting , layout , directed - undirected networks and more. Thanks a lot . Could you please explain the nested network and cytoscape automation ?
Thanks a lot! Regarding nested networks, they are quite easy to make: if you have a session with multiple networks, you can simple right-click a node in one network and choose another network to be put on that network (i.e. be nested). That allows you to make a network of networks, but I cannot think of a situation where I would want to do that, which makes it hard to make a compelling video about. Cytoscape automation is very useful, as it allows you to effectively "remote control" Cytoscape from a script, which can be great for making analyses reproducible. The problem from a video perspective is that it effectively becomes a programming video.
Thank you for this amazing videos, i am learning about biology networks and this help me a lot!!
Great to hear, I hope people learn a lot from me making these videos!
Great work~! If it is possible, could you please let me know what the best way you export the final 3D visualization for publication purpose? Thanks
I believe the only option at the moment is to do a screenshot. However, that is not as bad as it sounds. To get a "clean" image, you can get a white background by choosing the "Light" color scheme and turn off the coordinate system under Scene Actions. Given the resolution of modern monitors, you should get an image that is more than 300 dpi when printed the size of a figure in a journal. I wish it was possible to export as vector graphics, but I suspect it would be a lot of work to implement.
@@larsjuhljensen Thank you so much for the explicit answer~!
You teach everything in the easiest way. Because of you it has been possible to understand clusteting , layout , directed - undirected networks and more. Thanks a lot . Could you please explain the nested network and cytoscape automation ?
hello sir, can show also show a step by step video of how to make a hub gens-TF-miRNA network in cytoscape?
I cannot think of an elegant way to do this in just Cytoscape. Unless you first do some scripting to filter the miRNA network, you would have to import the entire network into Cytoscape. The latter is possible, but it would be very slow.
Dear Jensen thank you for the videos they are great explained.
Kindly can I get your email.
I need your help with some big data of protein concerns my study and I want to use Gene set enrichment analysis to classify them.
Thank you.
It's on my lab page: jensenlab.org/people/larsjuhljensen/