Eitan Rubin

11 Questions 48 Answers 0 Followers

Questions related from Eitan Rubin

How can I download germline variants info from TCGA?

I have access to controlled data. I have done this some years ago, but can't seem to figure out the new interface. Ideas?

10 October 2016 6,748 3 View

What do you think about the Lancet letter regarding Gaza?

Below is a letter I have sent to Elsevier, the publisher behind Lancer: To Mr. Reller, Vice President for Global Corporate Relations at Elsevier I share the feelings expressed in the letter sent...

10 October 2014 5,711 1 View

The cost of starting a new on-line journal?

I am trying to start a new journal. I hope to make it free-open access if I can raise funds for that. Does anyone have any idea how much that should cost? What's the minimal stuff? 1 full timer?...

08 August 2014 4,894 0 View

Is anyone familiar with running weka with a sun grid engine?

I am trying to use weka on our cluster, running sun grid engine. I installed Weka myself without root permission, and added CLASSPATH info to .rcsh. When I run a shell command invoking WEKA (with...

08 August 2013 2,273 4 View

Is anyone working on Personalized (precision) cancer medicine?

We are working on a new wiki for precision cancer medicine. If you are working in the field, please let me know what you think (registration is required): http://rubinlab.bgu.ac.il/pcm/

08 August 2013 635 2 View

Is my SNP on some commercial platform?

Does anybody know how to check if a new SNP is on ANY chip? I am looking for experiments in which a specfific SNP has been evaluated.

11 November 2012 953 4 View

How to align short reads to repetitive regions?

I am trying to align NGS data to repetitive regions. Straight-forward use of tools such as BWA fails. Any suggestions?

09 September 2012 1,375 6 View

Why are some nodes in Mega5 NJ tree shown without boostrap values?

My students noticed that you occasionally get no bootstrap values in a Mega5 tree. Bug? filtering? Any ideas? I attach the FASTA of the sequences used to generate the tree. Eitan

06 June 2012 9,363 15 View

How to compare the quality of clustering solution for the same dataset?

I always wondered how to test for the significance of clustering results. Now I have an urgent need. I want to show that when my input is organized in a biologically meaningful way. For that, I...

06 June 2012 3,035 15 View

Did anyone test the new compression tools for BAM format?

We have developed our own tool for compression, which saves ~70% while creating "regular" BAM files. But we are seeing all these new formats that are space economic - but I want to hear from...

05 May 2012 6,028 1 View

The math behind Oncotype?

I am going to present the Oncotype paper in a course, but in the NEJM paper they say “For this purpose, we used correlation analysis, dimension reduction, Martingale residual analysis, concordance...

01 January 1970 9,535 0 View