faq.gersteinlab.org
Gerstein Lab FAQs | Frequently Asked QuestionsFrequently Asked Questions
http://faq.gersteinlab.org/
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http://faq.gersteinlab.org/
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Gerstein Lab FAQs | Frequently Asked Questions | faq.gersteinlab.org Reviews
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Frequently Asked Questions
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ek | Gerstein Lab FAQs
http://faq.gersteinlab.org/tag/ek
Skip to primary content. Skip to secondary content. May 13, 2014. You should be able to download this software on a mac and use it. You can download it from funseq.gersteinlab.org. Since you are not familiar with downloading software, have you tried to use the online version at http:/ funseq.gersteinlab.org/analysis. You can upload your file and see what you get. Mutations in sensitive and ultra-sensitive regions. February 3, 2014. I can’t find them in the paper although they are mentioned. I would guess...
Annotation of SNPs as breaking or conserving TF motifs | Gerstein Lab FAQs
http://faq.gersteinlab.org/2013/12/11/annotation-of-snps-as-breaking-or-conserving-tf-motifs
Skip to primary content. Annotation of SNPs as breaking or conserving TF motifs. December 11, 2013. This makes perfectly sense to me. But how do you define the TF-binding site in the first place? I would guess that you are applying a threshold on the motif-matching score here (to reduce the fraction of false positives), and that you then define disruption/conservation of the variant relative to this score. I cannot see any details with respect to this aspect in the paper (as far as I can see). You are co...
rulefit3 in encodenets | Gerstein Lab FAQs
http://faq.gersteinlab.org/2013/05/30/rulefit3-in-encodenets-2
Skip to primary content. May 30, 2013. If the program is available for us, can you tell us the way to use it? In that paper we used the Rulefit3 package from Prof. Jerome Friedman; there is an R package available at the link below. Our use of the algorithm is extensively documented in Section C of the Supplementary Materials. Http:/ dx.doi.org/10.1214/07-Aoas148. Http:/ www-stat.stanford.edu/ jhf/r-rulefit/rulefit3/R RuleFit3.html. This entry was posted in clustering. Leave a Reply Cancel reply.
fosmid indel | Gerstein Lab FAQs
http://faq.gersteinlab.org/2013/05/31/fosmid-indel
Skip to primary content. May 31, 2013. I would like to ask about what kind of indels are incorporated into the. Diploid genome assembly of the NA12878 individual, available from your lab:. Http:/ sv.gersteinlab.org/NA12878 diploid/NA12878 diploid dec16.2012.zip. In the readme it says that 829,454 indels were used to construct this. Genome. What makes me confused is that when I perform a BLAST search with. One 17 kb deletion from NA12878.2010 06.and.fosmid.deletions.phased.vcf. Selected for this assembly?
clustering | Gerstein Lab FAQs
http://faq.gersteinlab.org/category/clustering
Skip to primary content. Skip to secondary content. May 30, 2013. If the program is available for us, can you tell us the way to use it? In that paper we used the Rulefit3 package from Prof. Jerome Friedman; there is an R package available at the link below. Our use of the algorithm is extensively documented in Section C of the Supplementary Materials. Http:/ dx.doi.org/10.1214/07-Aoas148. Http:/ www-stat.stanford.edu/ jhf/r-rulefit/rulefit3/R RuleFit3.html. Blog at WordPress.com.
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FAQ - GersteinInfo
http://info.gersteinlab.org/FAQ
How to Edit this. Our current FAQs page may be found here. Frequently asked questions about lab programs ( mailman version. Browse FAQ here http:/ groups.google.com/group/gerstein-lab-faqs? Regarding the Science paper titled Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights. The table headings unfortunately got switched at some unknown point during copy editing. We have posted a note to that point on our site. Do let me know if you need more help on this! MolMovDB: ...
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Gerstein Lab FAQs | Frequently Asked Questions
Skip to primary content. Skip to secondary content. ENCODE-Networks Source Code for Context-Specific TF Co-Association Analyses. June 7, 2014. Do you know whether the code for co-association analysis in this paper is available now? If so, it might save us a lot of time. Thanks for your help! The main machine learning method used for the analysis is RuleFit3 which is available here. Http:/ statweb.stanford.edu/ jhf/r-rulefit/rulefit3/R RuleFit3.html. May 13, 2014. February 3, 2014. I read your paper entit...
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