User: Janet Young
Janet Young • 730
- Reputation:
- 730
- Status:
- Trusted
- Location:
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Website:
- http://research.fhcrc....
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 months, 3 weeks ago
- Joined:
- 12 years, 1 month ago
- Email:
- j******@fhcrc.org
I provide bioinformatics support to members of Harmit Malik's lab. We work on a number of evolutionary questions using diverse tools.
Posts by Janet Young
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... thanks again. that makes sense (the mcols thing).
I'd better steer clear of identical! that's unpredictable and a little scary.
and yes, I'd made a wrong assumption about 'seq' - not sure where that came into my head from that it might be a function to get the seqs. It could have been the 'sho ...
written 3 months ago by
Janet Young • 730
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... Tried stackStringsFromGAlignments - looks great! Thanks again, Herve.
On a quick test it works really well. I did a sanity check with test alignment/region, and I noticed something that I'm sure I can ignore, but wondered if you might care about it for consistency.
I noticed on a test region tha ...
written 3 months ago by
Janet Young • 730
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... (deleted comment - meant to submit it as a reply) ...
written 3 months ago by
Janet Young • 730
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... Wow - so quick! thanks, Herve - really appreciate it.
It's been a while since I've used devel (things are so stable these days), so I'll have to remind myself how to run that, but I'll try this out ASAP.
Janet
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written 3 months ago by
Janet Young • 730
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... hi there,
It's been a while since I posted - hi all! I miss you bioc people here at the Hutch.
I am wondering whether a function exists that works like stackStringsFromBam, but operates on a GAlignments object (that contains a "seq" column) rather than a bam file. I'm asking because I want to d ...
written 3 months ago by
Janet Young • 730
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... Thanks, Michael - appreciate it. Yes, I'll start using github instead for stuff like this.
Maybe the github pages are worth a mention on http://www.bioconductor.org/help/support/posting-guide/ ?
...
written 18 months ago by
Janet Young • 730
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... Hi there,
I'm using rtracklayer's export function to get a bed file, and then I upload that file manually to the UCSC genome browser via my web browser.
I am using the trackLine/colorByStrand function - it seems to be almost working fine, but not quite. It would be great if the colorByStrand opti ...
written 18 months ago by
Janet Young • 730
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... done (https://github.com/Bioconductor/ensemblVEP/issues/2). thanks again!
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written 19 months ago by
Janet Young • 730
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... Thanks, Lori - that did let me troubleshoot successfully. I did just put in a github issue with a request to see the system call - that was really useful once you showed me how to do it using debugonce.
I should probably update to VEP v90 soon, but perhaps it's also useful to let you know where I s ...
written 19 months ago by
Janet Young • 730
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... Hi there,
This page - http://www.bioconductor.org/packages/release/bioc/html/ensemblVEP.html - says that the EnsemblVEP bioconductor package needs v88 of the Ensembl API, but from some of the help pages within ensemblVEP v1.20.0 it looks like maybe v90 is now supported too?
I'm asking because ...
written 19 months ago by
Janet Young • 730
• updated
19 months ago by
shepherl ♦♦ 1.6k
Latest awards to Janet Young
Popular Question
12 weeks ago,
created a question with more than 1,000 views.
For rtracklayer export: enable trackline for GRanges and RleLists, etc?
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18 months ago,
created a question with more than 1,000 views.
For Rgraphviz installation problem
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18 months ago,
created a question with more than 1,000 views.
For gviz: controlling track labels
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18 months ago,
created a question with more than 1,000 views.
For problem with cbind on GRanges object - new bug?
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18 months ago,
created a question with more than 1,000 views.
For rtracklayer export: enable trackline for GRanges and RleLists, etc?
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2.4 years ago,
created a question with more than 1,000 views.
For Rgraphviz installation problem
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2.4 years ago,
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For subset a RleList using GRanges object?
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For subset a RleList using GRanges object?
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created a question with more than 1,000 views.
For subset a RleList using GRanges object?
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For subset a RleList using GRanges object?
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3.2 years ago,
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For GenomicRanges request - enable ignore.strand for findOverlaps comparing query with itself?
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4.2 years ago,
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For tileGenome for overlapping ranges?
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