Moderator: karl.stamm

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karl.stamm3.2k
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Posts by karl.stamm

<prev • 428 results • page 1 of 43 • next >
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Comment: C: Rarefaction on R
... Okay maybe a Venn Diagram can show how many things are shared or unique between sets. But you have 17 groups, so that's a terrible mess. If it was 2-3 groups this could be a good visualization. With 17 groups, do you have any kind of experimental hypothesis? "Showing how diverse" could just be a ...
written 17 days ago by karl.stamm3.2k
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Comment: C: Rarefaction on R
... samples of what? A sample, to me is a tube of serum, how do you get more species than samples? what do you need from "test for richness" ? Sounds quite rich. ...
written 19 days ago by karl.stamm3.2k
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Comment: C: How representative the solid tumor sample is to that entire tumor lesion in term
... No, somatic mutations happen in individual cells, so you'll start with one cell with an arbitrary background, who suddenly evolves the ability to multiply quickly. It can become the majority of tumor mass. Its offspring may continue to mutate, or may stably reproduce the original. I think the firs ...
written 3 months ago by karl.stamm3.2k
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Comment: C: How representative the solid tumor sample is to that entire tumor lesion in term
... It's going to vary by tumor type. Fast growers will be homogeneous due to "clonality" but there's no measure of "the entire lesion". ...
written 3 months ago by karl.stamm3.2k
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Comment: C: Too many intronic variants in RNASeq, is this ok?
... Look more closely at your data. Depending on the alignment methods, maybe you have bits of RNA-transcript hanging off the end of an exon, and your tools see intronic mutations. I have seen piles of artifact intronic variants when the read was not trimmed from the end of an exon. It's not really the ...
written 3 months ago by karl.stamm3.2k
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Comment: C: Is DNA or RNA better to get somatic mutation profile for neoantigen estimation?
... What is a neoantigen? ...
written 5 months ago by karl.stamm3.2k
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Comment: C: Gene set enrichment analyses of different samples of the same species
... All genes are present in all stages, I can assure you the genome is not changing. What do you think enriched means? ...
written 5 months ago by karl.stamm3.2k
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Answer: A: MYH2 gene mutation location
... NM_017534 is on the reverse strand, so that CTC you're seeing on the genome is GAG on the transcript. You can see the little arrows go left in the intron of the alternate isoform, and the conservation track shows a lot in the right-most bases, indicating theyre the high order bit. And if you zoom o ...
written 6 months ago by karl.stamm3.2k
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Answer: A: BRIG: How to generate high resolution image
... Page 50 of the BRIG manual has a section called "Setting Image options" If those aren't enough, it is open source and you would have to hack it to do your preferred file format. ...
written 7 months ago by karl.stamm3.2k
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Comment: C: GC bias between samples tolerance in RNAseq?
... You've got bigger problems than GC content if you're trying to compare RNASeq between two different genomes. What is the experimental design? ...
written 7 months ago by karl.stamm3.2k

Latest awards to karl.stamm

Popular Question 12 weeks ago, created a question with more than 1,000 views. For Can I run VEP on a VCF twice?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
Appreciated 9 months ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Appreciated 12 months ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Scholar 16 months ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Appreciated 23 months ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Scholar 2.2 years ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Appreciated 2.2 years ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Appreciated 2.3 years ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Appreciated 2.4 years ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Scholar 2.6 years ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?

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