User: TriS

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TriS2.5k
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Posts by TriS

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Comment: C: How do you spend your time (productively) when your script is running?
... haha I didn't see the typo!! ...
written 5 days ago by TriS2.5k
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Answer: A: SomaticSniper VS Varscan2
... there are a number of papers out there comparing them (with other variant callers). examples are: [Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data][1] [Detecting somatic point mutations in cancer genome sequencing data: a comp ...
written 6 days ago by TriS2.5k
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Answer: A: How do you spend your time (productively) when your script is running?
... reading [Biostars][1] posts :) [1]: http://www.biostars.org ...
written 6 days ago by TriS2.5k
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Answer: A: AMAF, EMAF, and GMAF
... I love [google][1]: from Table2 of [this paper][2] MAF, minor allele frequency; AMAF, African American minor allele frequency; EMAF, European American minor allele frequency; GMAF, global minor allele frequency from [SNPedia][3] :) [1]: https://www.google.com/search?q=AMAF%2C%20EMAF%2C%20and% ...
written 12 days ago by TriS2.5k
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Answer: A: RNAseq heatmap.2 log2FC clustering
... scale your FPKM data before passing them to the heatmap. otherwise I like [pheatmap][1] m <- myFPKMdata pheatmap::pheatmap(m,scale="row") [1]: https://cran.r-project.org/web/packages/pheatmap/index.html ...
written 12 days ago by TriS2.5k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... hi Martin thank you for putting it on github, that's something I should have done a long time ago. and thank you for the updates as this post is more than one year old, I would expect to see some differences with what I posted at that time. clinical data are/should be updated and that will change, ...
written 16 days ago by TriS2.5k
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Answer: A: creating for loops in R for nGS data
... R solution: myData <- theResultsYouHaveAlready myDataFiltered <- myData[which(myData[,1] == myData[,4]),] awk awk -v FS='\t' -v OFS='\t' '{if($1 == $4) print}' myFileWithData.txt > myFileWithFilteredData.txt ...
written 18 days ago by TriS2.5k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... this question goes beyond what's described in this tutorial, you should start a new question in Biostar for that. ...
written 5 weeks ago by TriS2.5k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... it seems that there is a problem on the comment above where some brackets don't show up. pv <- ifelse ( is.na(s1),next,(round(1 - pchisq(s1$chisq, length(s1$n) - 1),3)))[[1]] ...
written 6 weeks ago by TriS2.5k
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Answer: A: Is it OK to select a small subset of expression data for statistical testing?
... it all depends from your rationale for choosing those genes. for example, if you choose genes that are g-protein coupled receptors and do functional enrichment analyses, you will find genes that are part of the g-protein coupled receptor pathways...and therefore your analysis will be futile. othe ...
written 8 weeks ago by TriS2.5k

Latest awards to TriS

Appreciated 5 weeks ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Scholar 9 weeks ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Epic Question 4 months ago, created a question with more than 10,000 views. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Popular Question 5 months ago, created a question with more than 1,000 views. For sample size, normality assumption, t.test/anova for DEG analysis
Gold Standard 5 months ago, created a post with more than 25 bookmarks. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Popular Question 8 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Popular Question 8 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?
Appreciated 9 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Great Question 10 months ago, created a question with more than 5,000 views. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Popular Question 11 months ago, created a question with more than 1,000 views. For Plot average methylation levels across TSS region
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Popular Question 11 months ago, created a question with more than 1,000 views. For Plot average methylation levels across TSS region
Appreciated 13 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Librarian 13 months ago, created a post with more than 10 bookmarks. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Diagnose my daughter?
Popular Question 13 months ago, created a question with more than 1,000 views. For Plot average methylation levels across TSS region
Scholar 14 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Scholar 14 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Guru 15 months ago, received more than 100 upvotes.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?

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