User: TriS

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TriS2.5k
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Posts by TriS

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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... the link was fixed, try using it now. basically those are information about which samples are normal or tumor ...
written 1 day ago by TriS2.5k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... thank you I appreciate it, i didn't realize the parenthesis was included ...
written 1 day ago by TriS2.5k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... which website? [firehose][1]? [1]: https://gdac.broadinstitute.org/ ...
written 2 days ago by TriS2.5k
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Comment: C: retrieve full TCGA datasets from cBioportal with R
... you can't get normals form cBioportal, you need to use [TCGA Firehose][1] [1]: https://gdac.broadinstitute.org/ ...
written 14 days ago by TriS2.5k
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Answer: A: retrieve full TCGA datasets from cBioportal with R
... Recently [cBioportal][1] allowed users to download full datasets, including mutations, clinical, methylation data etc etc... to retrieve use the "Summary" link on the right of the tumor type name and on the top part of the page you will be able to see a link saying "Download dataset"...click on that ...
written 20 days ago by TriS2.5k
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Comment: C: Current state-of-the-art for RNA-Seq gene / transcript expression quantification
... sleuth does have a way to work at the gene level (https://rawgit.com/pachterlab/sleuth/master/inst/doc/intro.html) furthermore, I used it recently for a few projects filtering only `transcript_biotype` as `protein_coding` from [biomaRt][1] and it seem to perform really well [1]: https://biocondu ...
written 25 days ago by TriS2.5k
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Answer: A: How to calculate the sum of ranks per gene??
... a lil more elaborated answer. if you use the ordered gene list as rownames you can use the following (I used letters as example): l <- LETTERS[1:6] m <- matrix(replicate(5,sample(l)),byrow=F,ncol=5) my_fun <- function(x){ initial_order <- x[order(x)] ranks ...
written 26 days ago by TriS2.5k
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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 6 weeks 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 weeks 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 weeks ago by TriS2.5k

Latest awards to TriS

Good Answer 25 days ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Scholar 3 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Epic Question 6 months ago, created a question with more than 10,000 views. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Popular Question 6 months ago, created a question with more than 1,000 views. For sample size, normality assumption, t.test/anova for DEG analysis
Gold Standard 7 months ago, created a post with more than 25 bookmarks. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Popular Question 9 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Popular Question 9 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Good Answer 10 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 10 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Great Question 11 months ago, created a question with more than 5,000 views. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Popular Question 12 months ago, created a question with more than 1,000 views. For Plot average methylation levels across TSS region
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Popular Question 12 months ago, created a question with more than 1,000 views. For Plot average methylation levels across TSS region
Appreciated 14 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Librarian 14 months ago, created a post with more than 10 bookmarks. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Diagnose my daughter?
Popular Question 14 months ago, created a question with more than 1,000 views. For Plot average methylation levels across TSS region
Scholar 16 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Scholar 16 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Guru 16 months ago, received more than 100 upvotes.

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