User: mar.ark.parr

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mar.ark.parr30
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Posts by mar.ark.parr

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Mapping NCBI Genome Accessions - NCBI Taxonomy IDs
... Thank you for the answer! ...
written 17 hours ago by mar.ark.parr30
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Comment: C: Mapping NCBI Genome Accessions - NCBI Taxonomy IDs
... Thanks a lot for the answer! ...
written 17 hours ago by mar.ark.parr30
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Mapping NCBI Genome Accessions - NCBI Taxonomy IDs
... Hi all, I have list of NCBI genome accessions (SAMN02441064, NC_014374, NZ_ACYB00000000 ...) and would like to know taxonomic IDs of the species that they belong to. Is there a mapping file somewhere? Or how can I find their taxonomic IDs programmatically? Thanks in advance, Marina ...
genome ncbi taxonomy genbank written 6 days ago by mar.ark.parr30 • updated 6 days ago by genomax70k
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SciClone on WES data
... Hello everyone! I have recently installed SciClone (https://www.biostars.org/p/246374/) and now trying to apply it to WES data of two tumors. Firstly, I used VarScan2 to call somatic variants, then I separate output file on germline, somatic or LOH. I took somatic (as vaf data) and LOH (as regions ...
dnacopy varscan clonality wes sciclone written 2.3 years ago by mar.ark.parr30 • updated 10 months ago by aliz06110
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Answer: A: SciClone installation in R version 3.3.3
... For anyone who will struggle with this problem :) This is what finally helped me. Combining what guys here wrote me and advices of the colleagues from my lab: When devtools library has been already installed and "install_github("genome/bmm")" done: `sudo rm -r /tmp/*` `sudo apt-get install libx11 ...
written 2.3 years ago by mar.ark.parr30
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Comment: C: SciClone installation in R version 3.3.3
... Santosh, I apologize for late response and thank you very much again for your help! But unfortunately even if i install X11 by the way you said, SciClone still doesn't see. It still has the same error with rgl and X11... So as I understood the possible solution is to try another R version... Older o ...
written 2.4 years ago by mar.ark.parr30
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Comment: C: SciClone installation in R version 3.3.3
... Thank you very much! Really decided to keep manual installation as plan B :) ...
written 2.4 years ago by mar.ark.parr30
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Comment: C: SciClone installation in R version 3.3.3
... Guys, thank you very much! Now using your advice I successfully moved to the last step of installation: install_github("genome/sciClone"). Currently it seems that the main problem is with rgl package: installing source package ‘rgl’ ... package ‘rgl’ successfully unpacked and MD5 sums checked check ...
written 2.4 years ago by mar.ark.parr30
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SciClone installation in R version 3.3.3
... Dear all! I plan to use SciClone to analyze cancer metastasis, but have problems while installation it. I have Ubuntu 16.04 and R version 3.3.3. I tried to follow instructions from https://github.com/genome/sciclone/blob/master/README.md and the error happens while installation package devtools: ...
R sciclone written 2.4 years ago by mar.ark.parr30

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Popular Question 2.3 years ago, created a question with more than 1,000 views. For SciClone installation in R version 3.3.3
Popular Question 2.3 years ago, created a question with more than 1,000 views. For SciClone on WES data

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