In silico Network Inference Last Improvements and Visualization of Result in Cytoscape

I’m almost done with the analysis of in silico data, although I need to decide if I need further analysis with the inhibiting parent nodes in the network. Last, I couldn’t filter out duplicate edges, which were scored differently. Now, with some improvements in the script, low scores duplicates are filtered and there is a better final list of edges which is ready to be visualized.

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Some String Functions in R, String Manipulation in R

I have programmed with Perl, Python, and PHP before, and string manipulation was more direct and easier in them than in R. But still there are useful functions for string manipulation in R. I’m not an expert in R but I’ve been dealing with it for a while and I’ve learned some good functions for this purpose.

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Webinar on HPN-DREAM Breast Cancer Network Inference Challenge

DREAM8 organizers plan a webinar about HPN-DREAM Breast Cancer Network Inference Challenge on July 19, at 10:30 - 11:30 (PDT / UTC -7). General setup of the challenge, demo submissions to the leaderboard will be discussed and also questions about the challenge will be accepted during webinar. The number of the participants to the challenge is also announced: 138.

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Network Inference Challenge in silico Data

I had a meeting with BiGCaT this week and we discussed DREAM Breast Cancer Challenge. I presented the challenge and also some ways that I have found to solve the first sub-challenge network inference. Tina, from BiGCaT, suggested starting with in silico data which is much simpler than breast cancer data. Later, I can use the methods I develop for in silico data in experimental data.

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Playing around with CellNOptR Tool and MIDAS File

With CellNOptR, we will try to construct network models for the challenge. For this, the tool needs two inputs. First one is a special data object called CNOlist that stores vectors and matrices of data. Second one is a .SIF file that contains prior knowledge network which can be obtained from pathway database and analysis tools.

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