User: aush

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aush40
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New User
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United States
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6 months, 3 weeks ago
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3 years, 11 months ago
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Posts by aush

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Comment: C: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
... Thanks again! 1) In this particular case I don't have raw data, I have to work with what I have. I will definitely consider using annotateEset if I get .cel files! 2) Sure, I looked at the help page - but it was not explaining how exactly the mapping is done in this case. From your explanation, now ...
written 14 months ago by aush40
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Comment: C: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
... James, thank you so much for your fast and informative reply! If I may post couple additional questions: 1) I was actually using mget() in my real code - it is also considered old interface? I use data.table, and my command was as following: dt.dat[, ratSym1:=mget(transcriptID,ragene20sttranscriptcl ...
written 14 months ago by aush40
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Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
... I am trying to figure out why thousands of transcript clusters are not mapped in ragene20sttranscriptcluster.db while they are perfectly present in the manufacturer's materials. Just one example: transcriptcluster 17610996 is well described in the manufacturer's annotation (support files at https:// ...
ragene20sttranscriptcluster.db written 14 months ago by aush40 • updated 14 months ago by James W. MacDonald51k
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Comment: C: blastn for selected database and/or organism
... Thank you James! I have contacted NCBI support, and the solution turned out to be quite simple: besides QUERY, their API supports a field ENTREZ_QUERY. Unfortunately it is not included in annotate for now, but I simply added &ENTREZ_QUERY=human%5borgn%5d string to my QUERY, and this worked! ...
written 17 months ago by aush40
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blastn for selected database and/or organism
... Is there any way to blast my nucleotide sequence only against specific NCBI database, for example, refseq_rna? Similarly, I'd like to limit my search to a specific organism/taxid.   As I understand, blastSequences() doesn't have these options now. Is there any other solution? ...
blast blastsequences written 17 months ago by aush40 • updated 17 months ago by James W. MacDonald51k
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resize (shrink/expand) GenomicRanges
... I have a set of `GenomicRanges` and all I need is to expand it by certain distance on start and another distance on end (taking into account the strand). For example, from this set:   strand start end 1    + 100 110 2    - 200 220 3 ...
iranges genomicranges written 3.7 years ago by aush40 • updated 3.7 years ago by Hervé Pagès ♦♦ 14k
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How to get 'previous symbols'? is there HGNC Mart connection?
... In the HGNC database, there are "Previous symbols & names" and "Synonyms" fields which I would like to retrieve for my genes. I wanted to use biomaRt for that, but I don't know if HGNC mart exists (biomart.org portal doesn't work since Thursday, so I can't even run listMarts()), or if I can get ...
biomart hgnc written 3.9 years ago by aush40 • updated 3.9 years ago by Gordon Smyth38k
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"Error: object 'nuID' not found" error when using `returnAllMatches=TRUE` in `IlluminaID2nuID()`
... When I try to execute IlluminaID2nuID(), something like this: IlluminaID2nuID("ILMN_11214", returnAllMatches=TRUE) IlluminaID2nuID("ILMN_16343", returnAllMatches=TRUE) - I get an error: "Error: object 'nuID' not found" (for both examples). I googled but could not find any information about this e ...
lumi lumihumanidmapping written 3.9 years ago by aush40
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no chip information in lumiHumanIDMapping?
... I was trying to use `IlluminaID2nuID()` and found that for some of my IDs I can't get any information at all (for example, `getChipInfo('ILMN_163950')` gives "No matches were found!" message). Then I noticed that for other IDs I can get info, but this does not include the chip we actually had: for e ...
lumi lumihumanidmapping written 3.9 years ago by aush40

Latest awards to aush

Popular Question 14 months ago, created a question with more than 1,000 views. For How to get 'previous symbols'? is there HGNC Mart connection?
Student 14 months ago, asked a question with at least 3 up-votes. For resize (shrink/expand) GenomicRanges
Popular Question 3.6 years ago, created a question with more than 1,000 views. For resize (shrink/expand) GenomicRanges

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