Cytoscape 3 Quickstart Tutorial - Basic Expression Analysis

  Рет қаралды 104,585

Trey Saddler

Trey Saddler

Күн бұрын

Пікірлер: 23
@arkodasgupta9608
@arkodasgupta9608 6 жыл бұрын
Most helpful Cytoscape tutorial I have come across! Cheers!
@MalithArambage
@MalithArambage 5 ай бұрын
This video is Excellent. To the point, simple and clear! Thanks mate!
@humarafique3093
@humarafique3093 2 ай бұрын
Hi, I only have genes list, how can i make my input like this what you've shown in the video as input file.csv?
@noorulain7302
@noorulain7302 4 жыл бұрын
you should also teach how to arrange a particular data set for input. using sample data is so confusing for me
@mehwishwahid183
@mehwishwahid183 3 жыл бұрын
hi can someone guide me how can I save my analysis results in excel file using cytoscape
@sumitkumar-el3kc
@sumitkumar-el3kc 4 жыл бұрын
How can I identify non-human proteins in a given network in Cytoscape?
@jagdishchand9321
@jagdishchand9321 4 жыл бұрын
Hello can you help me to make my excel sheet data of my own synthesized compounds.
@gershonanim6072
@gershonanim6072 2 жыл бұрын
HI Trey, I do not find the shared interaction on my version (3.9.1). where could it be
@TreySaddler
@TreySaddler 2 жыл бұрын
It seems like it really is time for me to make a new video. Many things have changed inside Cytoscape since I first made this one. So I'm not 100% sure where the shared interaction thing would be at this moment but I will get back to you on that.
@gershonanim6072
@gershonanim6072 2 жыл бұрын
@@TreySaddler Thanks so much. I found it.
@WhiteHFS
@WhiteHFS 4 жыл бұрын
My COMMON column appears invisible. I mean, no data is visualized
@KainBAl
@KainBAl 3 жыл бұрын
hi Trey Saddler very good and informative tutorial!!!! Can I ask you a question? I am new to cytoscape and I am trying to learn how to use it. When you import a String network into cytoscape and I want to see protein clusters in that network. How can I then assign a specific biological function to a specific group of proteins. I mean rather, as I have seen in some papers, which show a network and then they circulate, for example, in red, different groups of proteins with their specific biological function. How can i achieve this?
@chowdhurymh5527
@chowdhurymh5527 5 жыл бұрын
Can you do one detail tutorial covering network with edge weight, network co-ordinate, centrality measurememt, etc? Like what cytoscape example network looks like, but don't know how to do that. So it would be much appreciated and helpful for us....
@TreySaddler
@TreySaddler 5 жыл бұрын
Sure, will do!
@chowdhurymh5527
@chowdhurymh5527 5 жыл бұрын
Hi Trey, Thanks. It would great if you could do it as soon as possible. Thanks
@johirislam8174
@johirislam8174 3 жыл бұрын
Hi,I want to visualize my PPI network into cytoscape.But my ppI node are 661 and edges are 680 and seeds are 15.So i feel problem of visualizing it into cytoscape.Because of huge number of nodes and edges. So how can i visualize this .I mean to say I want to know the way that can visualize all the interacted nodes clearly. Clearly means all the lebels are being clearly watched in manuscript.
@TreySaddler
@TreySaddler 3 жыл бұрын
You can experiment with changing node and edge parameters, such as transparency, size, and color to try and emphasize certain features. But in general the best strategy to try and create a more usable network is to reduce or group the number of nodes and edges if possible, or to only display labels for the nodes that are most important.
@johirislam8174
@johirislam8174 3 жыл бұрын
@@TreySaddler which basis i should reduce the noded and edges?And how can i only display the nodes?
@imrankhanbbt
@imrankhanbbt 5 жыл бұрын
Great work, and most helpful.. thank you
@adibshaheen343
@adibshaheen343 2 ай бұрын
you are not explaining why u r doing each step tho :(
@yeyefortcheka
@yeyefortcheka 5 жыл бұрын
thank you!
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