User: gnmcsbnfrmtcsclb

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Posts by gnmcsbnfrmtcsclb

<prev • 19 results • page 1 of 2 • next >
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Comment: C: learning human genetic predictions using genome vs. ClinVar
... Thank you, gonna use recommendations from you and JC to learn new concepts, may take us at least a few weeks of learning from tutorials with some small and smple test cases to even start the analysis we envision. At that time, we will post any follow up questions / doubts. Also, we think it may be b ...
written 7 days ago by gnmcsbnfrmtcsclb30
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Comment: C: learning human genetic predictions using genome vs. ClinVar
... Thank for so much for your systematic replies. Our goal is to learn, so we thought free data, would be interesting to just help us learn. So we will try out those software as a learning exercise in both theoretical concepts and practical analyses. Usually, for human genome, with only 30X coverage, ...
written 8 days ago by gnmcsbnfrmtcsclb30
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Comment: C: learning human genetic predictions using genome vs. ClinVar
... Thank you for your response. Is there a scientific consensus about the minimum acceptable fold coverage for sequencing in order to draw clinically related conclusions? And is there an open source database like ClinVar that folks use and prefer over ClinVar? Thanks again. ...
written 8 days ago by gnmcsbnfrmtcsclb30
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learning human genetic predictions using genome vs. ClinVar
... We are a group of ~ 20 rising sophomore and juniors that are interested in group learning of new and interesting concepts in genetics and genomics. We seek your help with answers to the following questions please, about analyzing human genome sequences. A little context: One student in our group ha ...
genome clinvar genotype rna-seq written 9 days ago by gnmcsbnfrmtcsclb30 • updated 9 days ago by JC11k
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Comment: C: deepTools NPZ to PCA plot with modifications
... Thank you Prof. Ryan!. We are so glad to be on a free-of-cost BioStars forum, with such helpful forum members as yourself. We can learn so much by doing, rather than just sitting in classroom lectures. This is way more fun! :) ...
written 10 weeks ago by gnmcsbnfrmtcsclb30
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Comment: C: deepTools NPZ to PCA plot with modifications
... Super awesome, we understood every one of your simplified and clear replies, thanks a lot! :) **One final request** : could you confirm / correct our syntax below, for `bamCoverage` and `multiBigwigSummary`? bamCoverage -b $IN.bam -o $OUT.bw --normalizeUsing None --effectiveGenomeSize $ACGTon ...
written 10 weeks ago by gnmcsbnfrmtcsclb30
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Comment: C: deepTools NPZ to PCA plot with modifications
... Dear Prof. Ryan We agree! Initially, input of NPZ files into R was such a pain, but the R 'reticulate' package ain't so bad, even for us R noobs :) However, we've now managed to confuse ourselves :) Could you please help clear our confusion with perhaps some (made-up) numbers to help us understan ...
written 10 weeks ago by gnmcsbnfrmtcsclb30
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Comment: C: deepTools NPZ to PCA plot with modifications
... Thank you for your clarification, Prof. Ryan. Since our original post, and before your response here, this is what we tried. 1. Unzip the NPZ output of `deepTools`' `multiBigWigsummary`, 2. Read in resulting separate matrix and labels NPY files in `R` using the `reticulate` package, bind the ...
written 10 weeks ago by gnmcsbnfrmtcsclb30
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deepTools NPZ to PCA plot with modifications
... Is it possible to modify the plotPCA output of `deepTools` as follows? 1. Suppress the SCREE plot completely 2. Label the points with user supplied names that are already found in the default legend 3. Ensure labels do not overlap (with something like `ggrepel`) 4. Control font size of output ...
deeptools plotpca written 11 weeks ago by gnmcsbnfrmtcsclb30 • updated 10 weeks ago by Devon Ryan97k
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Comment: C: map gene gain loss on species tree
... http://www.ub.edu/softevol/badirate/ I suppose this is the software that https://www.biostars.org/u/65659/ is referring to? ...
written 7 months ago by gnmcsbnfrmtcsclb30

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