User: tomoya

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tomoya0
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Posts by tomoya

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Extracting annotation information from EntrezID
... Thank you for several suggestions and I successfully earn the annotation information by using this command. ...
written 21 days ago by tomoya0
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Extracting annotation information from EntrezID
... Now I have several EntrezIDs list (ex. 101171905, 101164258, 101173884, ...). By using this list, I'd like to add several information (gene name, gene symbol and description) to these lists. I know one of the way to extract these information is Biomart, but I would like to use NCBI database because ...
gene R written 4 weeks ago by tomoya0 • updated 29 days ago by BBioinf0
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Comment: C: Convert RefseqID to EntrezID
... Oh, I already get the results. Thank you for pointing out! Sorry for several times, I still have one more question. The order of outputs is not same to inputs. So I'd also like to keep the order of outputs or extract both (refseqID and EntrezID in a same order) to find out which refseqID is link t ...
written 9 weeks ago by tomoya0
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Comment: C: Convert RefseqID to EntrezID
... Sorry for twice. I notice I need to reply like this. I see. I need to specify the format, but I still struggling how to specify "uid" by reutils. ...
written 9 weeks ago by tomoya0
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Comment: A: Convert RefseqID to EntrezID
... Thank you very much, both of you for your comments. I understand this is because these genes are not include in current Ensembl release and EDirect can solve this. Thanks to vkkodali comment, I notice if I want to use EDirect by R, I can use reutils or rentrez. And I tried below command learning fr ...
written 9 weeks ago by tomoya0
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Comment: A: Convert RefseqID to EntrezID
... Thank you for many suggestions! These are very useful for me and I successfully get almost all EntrezIDs by using biomaRt. However, I still have some questions. Although I get almost all EntrezIDs, some are missing (results show NA). For example, XR_002293119.2 or XM_004081009.3 or XM_023961859.1. ...
written 9 weeks ago by tomoya0
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Convert RefseqID to EntrezID
... Hi, I have a set of genes with Refseq ids (ex. XM_020713141.1) and I want to convert it to EntrezID (ex. 101165603) for further analysis. I find similar question that said clusterProfiler is suitable for this purpose. [https://www.biostars.org/p/163301/][1] However, I'd tried to find out Medaka (Ory ...
gene R written 9 weeks ago by tomoya0
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Comment: C: rMATs error: unknown file type
... Thank you very much for your kind support! I figured out that rMATS 4.0.2 doesn't support MacOS now. So I decided to use the previous version (rMATS 3.2.5) and it works. ...
written 4 months ago by tomoya0
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Comment: C: rMATs error: unknown file type
... I tried gcc-6, however, I still have the same error (My operating system is macOS ver. 10.14.2). I also installed lumpy, Blas, lapack and gsl again but the result was same. Do I have to do something except moving rMATS.4.0.2 file to working directory for using rMATS correctly? Also, does python ver ...
written 4 months ago by tomoya0
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Comment: C: Some problems using rMATs
... Thank you for your suggestion. I followed the installation guidelines and found installing gcc@5 seems to be failed. I got the below error: xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun ...
written 4 months ago by tomoya0 • updated 4 months ago by WouterDeCoster40k

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