User: Nathan Sheffield

Reputation:
10
Status:
New User
Location:
University of Virginia
Website:
http://www.databio.org/
Last seen:
1 month, 2 weeks ago
Joined:
3 years, 2 months ago
Email:
n*****@code.databio.org

Posts by Nathan Sheffield

<prev • 11 results • page 1 of 2 • next >
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Comment: C: What's the best way to retrieve the sizes (lengths) of chromosomes for a referen
... Thanks, that could be exactly what I need... out of curiosity, is there a way to get assembly gaps out of GenomeInfoDb the way you can from a BSgenome object? I didn't see that so far... ...
written 3 months ago by Nathan Sheffield10
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What's the best way to retrieve the sizes (lengths) of chromosomes for a reference genome assembly?
... When I need to know the total sizes of chromosomes, I typically use the `BSGenome` package, which provides both metadata (like seqnames(BSgenome)) as well as raw sequence data. I'm building a package now that needs this metadata information -- but for a package that never needs the raw sequence dat ...
bsgenome reference genome chromosome written 3 months ago by Nathan Sheffield10 • updated 3 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: GOTHiC hg19 error
... Upgrading to the latest version solves the problem. ...
written 2.7 years ago by Nathan Sheffield10
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Comment: C: GOTHiC hg19 error
... you can fix the bug, maybe, with something like this: w = which(ends-starts > 0) resGR <- GRanges(seqnames = chrs[w], ranges = IRanges(start = starts[w], end = ends[w])) ...
written 2.7 years ago by Nathan Sheffield10
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GOTHiC hg19 error
... Hi, I think I may have found a bug in GOTHiC. It does not seem to work with hg19, while it works fine with hg18, independent of the input, restriction site, etc. You can reproduce this error by just using the vignette sample, but switching the genome from hg18 to hg19. The input files doesn't reall ...
gothic hic written 2.7 years ago by Nathan Sheffield10
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Comment: C: Bioconductor Docker Development container
... btw, it's in the "checking PDF version of manual" where the errors come in, not vignettes... here's an example from a package with only Rmd vignettes: * checking running R code from vignettes ...    'choosingUniverse.Rmd' ... OK    'gettingStarted.Rmd' ... OK    'usingLOLACore.Rmd' ... OK  OK * che ...
written 3.0 years ago by Nathan Sheffield10
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Comment: C: Bioconductor Docker Development container
... Thanks -- I'll give it a try. But I'm a bit confused now -- actually, all my vignettes are written in markdown (Rmarkdown to be precise, .Rmd) -- yet when I run R CMD check, it builds PDF versions, requires qpdf/pdflatex etc... But your comment indicates that these are only needed for vignettes wri ...
written 3.0 years ago by Nathan Sheffield10
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Bioconductor Docker Development container
... Hi, I'm trying to use the bioconductor containers listed here: http://www.bioconductor.org/help/docker/ and announced by @Dan Tenenbaum here: https://support.bioconductor.org/p/63978/ I want to use the devel container to build R packages... the problem is since the bioconductor/devel containers are ...
bioc-devel docker written 3.0 years ago by Nathan Sheffield10 • updated 3.0 years ago by Dan Tenenbaum ♦♦ 8.2k
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Comment: C: IRanges missing S4Vectors_defines.h
... @Hervé Pagès  Incidentally, since you're an author of IRanges, would you be interested in accepting a code contribution to add this functionality from IRangeKernels directly into IRanges? It's a small update... Then I wouldn't have to worry about these packing and linking issues... and maybe others ...
written 3.2 years ago by Nathan Sheffield10
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Comment: C: IRanges missing S4Vectors_defines.h
... @Hervé Pagès Thanks for the advice. After updating R, and all bioC stuff with `biocLite()`, I still have the same error on the release version, and also on the devel version. -- I discovered that the issue only happens when I use install_github, but goes away when I clone and install locally, so per ...
written 3.2 years ago by Nathan Sheffield10

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