User: TriS

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TriS3.0k
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Posts by TriS

<prev • 320 results • page 1 of 32 • next >
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Comment: C: Concatenate RNA-seq technical & biological reps or just technical reps before al
... for DE transcripts keep the biological replicates separated, align them separately and then calculate DETs/DEGs. for SNPs I'd suggest to do a similar approach. call SNPs per each replicate and keep those common across biological replicates. ...
written 18 days ago by TriS3.0k
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Comment: C: DESeq2 Heatmap issue
... figure margins too large make the figure smaller and try again png("qc-heatmap-samples.png", w=500, h=750) ...
written 22 days ago by TriS3.0k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... this should be posted as a new question since it's not specific for this tutorial. anyhow..1) how does `head(rna)` look? 2) it seems you don't have a design matrix `d` 3) how many genes are in `rna`? ...
written 5 weeks ago by TriS3.0k
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Comment: C: Is there a way to calculate p-values, FDR or t test starting from logFC data?
... you don't need raw count values, you can use TPM and limma to get DEGs ...
written 7 weeks ago by TriS3.0k
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Answer: A: Is there a way to calculate p-values, FDR or t test starting from logFC data?
... it's a (partial) duplicate question from here: https://www.biostars.org/p/248383/ here https://www.biostars.org/p/8945/ see answers there. also from Google: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728800/ https://www.bioconductor.org/help/workflows/rnaseqGene/ http://biocluster.ucr.edu/~r ...
written 7 weeks ago by TriS3.0k
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Answer: A: B Cell Epitope Prediction: Maximizing Antigenicty and Minimizing Sequence Lengt
... immunogenicity prediction is a very uncharted territory. that is, a potential antigenicity (or peptide recognition by the MHC) still does not tell you whether your lymphocytes have the receptor's repertoire (TCR or BCR) to recognize the peptide. this means that once you move into in vitro and in viv ...
written 7 weeks ago by TriS3.0k
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Answer: A: CPM and FPKM value
... simple and to the point, thank you Google: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/ ...
written 7 weeks ago by TriS3.0k
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Comment: C: secondaryFiles for bam: how to handle .bai or/and ^.bai ?
... are you trying to get the files that end with either bam.bai or .bai? if that's the case just grep out those with .bai.... how are your writing your workflow? unix shell? ...
written 8 weeks ago by TriS3.0k
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Answer: A: Download data from TCGA
... easiest way: 1. go to cBioportal 2. click on the tumor type you want 3. on the right side click on "summary" 4. on the top of the page you have "download data" ..there you go ...
written 8 weeks ago by TriS3.0k
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Answer: A: TCGA: Stratify breast cancer cases based on presence of Her2 mutation and get tr
... simplest ways: go to cBioportal --> select your tumor type --> click on the right inside the link for "summary" --> on the top click the "download data" 1) from here open the mutation data, skim for Her2 and get the corresponding patient IDs then open the RNASeq data and select out th ...
written 8 weeks ago by TriS3.0k

Latest awards to TriS

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Scholar 6 weeks ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Diagnose my daughter?
Scholar 10 weeks ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Popular Question 3 months ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Scholar 4 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Popular Question 4 months ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Good Answer 5 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 5 months ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Good Answer 6 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 8 months ago, created a post with more than 5 votes. 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?
Scholar 9 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Epic Question 12 months ago, created a question with more than 10,000 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 sample size, normality assumption, t.test/anova for DEG analysis
Gold Standard 13 months ago, created a post with more than 25 bookmarks. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Popular Question 15 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Popular Question 15 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Good Answer 16 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 16 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
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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