User: Sirus

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Sirus730
Reputation:
730
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Location:
Boston/USA
Website:
http://www.bioinfo4ara...
Last seen:
2 days, 16 hours ago
Joined:
6 years, 6 months ago
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Bioinformatics student

Posts by Sirus

<prev • 73 results • page 1 of 8 • next >
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Comment: C: StackExchange/Area51 bioinformatics is back
... It is much more different, bioconductor support is mainly to help with the questions related to bioconductor packages and R programming in bioinformatics, while Biostars is a general bioinformatics plateform. A new SE site similar to biostars will not bring any thing new. ...
written 3 days ago by Sirus730
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Answer: A: intersect multiple bed files in R
... You can use the `findOverlapsOfPeaks` function from the [ChIPpeakAnno][1] package. Just to make the code more easy to follow, I use the `readBroadPeak` function from the genomation package. But you don't need to use too many packages to do that. Suppose you have 3 bed files in the boradPeak forma ...
written 5 weeks ago by Sirus730
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Comment: C: without normal control, can I know a gene's expression level only by its express
... Are they from the same tumor or they are different ones ? ...
written 13 months ago by Sirus730
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Comment: C: Chip-Seq, Get Highly Enriched Regions For A Certain Mark Within One Sample
... Yeah,  A more elaborated model is in the jmosaics model  http://www.genomebiology.com/2013/14/4/R38 ...
written 15 months ago by Sirus730
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Answer: A: Plotting large PPI biological networks
... For big networks visualization, I think R is not the best choice, you can save it in R as gml format of a ncol format (if you don't have attributes in your nodes) and visualize it in some specialized tools such as Gephi. ...
written 19 months ago by Sirus730
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Answer: A: Why we need two instead of one kinds of Linkers in ChiA-PET?
... Hi chenxiaoyu4,  The answer is 5 weeks after your post, but maybe it will be helpful for others.  The idea behind using two linkers is to estimate random interactions. If you just use linker A and then do the mapping, you cannot know which interaction is real and which one is just a result of ran ...
written 2.4 years ago by Sirus730
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Answer: A: Combing two microarray datasets
... It seems there is a problem with the code (maybe was not updated by the authors) I did the following changes in the `virtualArrayBuildfData` function, I remove the lines 62 and 63 : rownames(exprs_z$data) <- exprs_z$labels[[1]][, 1] colnames(exprs_z$data) <- exprs_z$labels[[2]][, 1] exprs_z ...
written 2.4 years ago by Sirus730
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Comment: C: Chip-Seq, Get Highly Enriched Regions For A Certain Mark Within One Sample
... In my case I want the threshold to be dynamic for each mark, in this way I can annotate which parts are at the same time H3K4me1+, H3K4me3-,... etc So I thought I can for each mark do the classification, and I can select any combination and just do the intersection. for the moment I am using the Poi ...
written 3.1 years ago by Sirus730
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Comment: C: Chip-Seq, Get Highly Enriched Regions For A Certain Mark Within One Sample
... Hi Albert, Thanks for the paper :). However, they talk about differential binding and comparing peaks between different samples. In my case I have just one sample in one condition and I want to find which peaks within my sample have significant hight enrichment to classify them into highly and lowl ...
written 3.1 years ago by Sirus730
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Chip-Seq, Get Highly Enriched Regions For A Certain Mark Within One Sample
... Hi guys, When reading through many papers, I see many people people mentioning features like H3K4me1+ (or hight), H3K4me3-,.... etc, generally they don't say how they did it automatically to find these regions. To make the picture clear, my situation is as follow: I have some Chip-Seq data (One s ...
enrichment chip-seq written 3.1 years ago by Sirus730

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