User: TriS

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TriS2.9k
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Posts by TriS

<prev • 308 results • page 1 of 31 • next >
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Answer: A: Comparison between multiple fasta files in terms of presence or absence of certa
... two approaches you could try are in perl and unix perl: [from previous question in biostar][1] UNIX: [AWK solution][2] [1]: https://www.biostars.org/p/4346/ [2]: https://stackoverflow.com/questions/28289363/awk-solution-for-pattern-matching-and-allowing-one-ambiguity-mismatch ...
written 8 hours ago by TriS2.9k
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Answer: A: Urgent request - Pipeline for finding somatic and germline mutations of a cancer
... a little bit of disclaimer first, just for safety: here we do NOT provide information that lead to choosing or altering a medical treatment, all info are for educational purpose and the investigator assumes the final responsibility of what to do with the info provided. that said...what you did in t ...
written 5 weeks ago by TriS2.9k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... you can assign groups to patients that have high/low expression, i.e. high=1, low=2, middle=0, remove the 0s and run survival as above. as warm suggestion, look a lil more into how to run survival analyses in R, don't just copy and paste the code above without knowing what's doing what. that will b ...
written 5 weeks ago by TriS2.9k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... the description is in the voom paper "[voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Charity W Law, Yunshun Chen, Wei Shi and Gordon K Smyth][1]" for my understanding voom keeps in consideration the experimental design, i.e. treatments/replicates/etc, to weight ...
written 5 weeks ago by TriS2.9k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... that is pretty simple, use disease free survival data, generally as DFS in the clinical data. then there should be a column saying "tumor free/with tumor". ...
written 5 weeks ago by TriS2.9k
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Comment: C: Problem with Manhattan plot
... how do your data look? what's the code that you used? I suppose you are using R for the plot? what does the image look like (we can't see it, or at least I can't)? hard to help without info ...
written 9 weeks ago by TriS2.9k
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Answer: A: DESeq2: Find differentially expressed genes specific to one condition
... I had a similar situation, I used limma, not DESeq2 but the concept is the same. the first thing I did was to use your approach #1, which worked fine. then I started working on the contrast matrix. let's say your data look like > data A A B ...
written 9 weeks ago by TriS2.9k
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Answer: A: RNA-seq analysis with quantitative traits
... this is also a good read for your analysis [RNA-seq analysis for detecting quantitative trait-associated genes][1] [1]: https://www.nature.com/articles/srep24375 ...
written 9 weeks ago by TriS2.9k
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Comment: C: BWA: Why paired reads mapped to different chromosome?
... fusion gene event could cause that. are those cancer samples? ...
written 9 weeks ago by TriS2.9k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... hmmm, ok, try to run `s1` and `summary(s1)` you should get something like the following > s1 Call: survdiff(formula = f ~ a) N Observed Expected (O-E)^2/E (O-E)^2/V a=1 77 44 45.5 0.0464 0.0794 a=2 106 69 67.5 0.0312 0.0794 ...
written 11 weeks ago by TriS2.9k

Latest awards to TriS

Teacher 11 days ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Scholar 11 days ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Popular Question 19 days ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Popular Question 7 weeks ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Scholar 9 weeks ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Popular Question 9 weeks ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?
Popular Question 3 months ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Good Answer 4 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 6 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Appreciated 6 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Scholar 7 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Epic Question 10 months ago, created a question with more than 10,000 views. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Popular Question 10 months ago, created a question with more than 1,000 views. For sample size, normality assumption, t.test/anova for DEG analysis
Gold Standard 11 months ago, created a post with more than 25 bookmarks. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
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 13 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Popular Question 13 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Good Answer 14 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 14 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Great Question 15 months ago, created a question with more than 5,000 views. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Popular Question 16 months ago, created a question with more than 1,000 views. For Plot average methylation levels across TSS region
Teacher 16 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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