Admin: shepherl

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shepherl ♦♦ 240
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Posts by shepherl

<prev • 36 results • page 1 of 4 • next >
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Answer: A: Parallel reading of Vcfs using VcfStack/RangedVcfStack
... Thank you very much for your interest.  We think this is a good suggestion and will look at implementing sometime during the next month.  ...
written 1 day ago by shepherl ♦♦ 240
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News: ensembl 87 and 88 gtfs and fasta twobits have been added to AnnotationHub
... Hello all,  The ensembl 87 and 88 gtfs (converted to GRanges on the fly) have been added to AnnotationHub and are currently available: > library(AnnotationHub) > hub = AnnotationHub() updating metadata: retrieving 1 resource |============================================================== ...
annotationhub news bioconductor written 16 days ago by shepherl ♦♦ 240
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Comment: C: R getting "stuck" with RoadMap resource retrieval through AnnotationHub
... No problem.  We've all dealt with slow network issues.  Feel free to post more if you find you are having any other issues.  ...
written 20 days ago by shepherl ♦♦ 240
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News: Bioconductor Dockers Updated
... The bioconductor dockers have been updated for the release.  The release versions now utilize R 3.4.0 and Bioc 3.5 while the devel versions now utilize R 3.4.0 and Bioc 3.6.  Older versions are available using tags.  For more information on Bioconductor dockers please see http://bioconductor.org/hel ...
news bioconductor docker written 20 days ago by shepherl ♦♦ 240
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Comment: C: R getting "stuck" with RoadMap resource retrieval through AnnotationHub
... I'm still having trouble reproducing as I can run your code above with no issues.  What is your output of sessionInfo()? We want to make sure you are using the most updated versions of all the packages for your version of R, you can check by using biocLite().  From the look of the snapshot date of A ...
written 20 days ago by shepherl ♦♦ 240
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Answer: A: R getting "stuck" with RoadMap resource retrieval through AnnotationHub
... I also cannot reproduce the problem.  Could you please provide the exact code you ran as well as the results of sessionInfo().  ...
written 21 days ago by shepherl ♦♦ 240
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News: Single Package Builder Upgrade
... Over the next week,  we will be transitioning the Single Package Builder to the latest versions of R and Bioc 3.6. The single package builder is used when new packages are submitted to:  https://github.com/Bioconductor/Contributions .  Please be advised that there may be intermittent periods where t ...
news bioconductor written 22 days ago by shepherl ♦♦ 240
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Answer: A: Bioconductor RNA-seq bed file read-in/download then wavelet transform
... The Bioconductor package rtracklayer provides for reading in bed files.   source("https://bioconductor.org/biocLite.R") biocLite("rtracklayer") library("rtracklayer") ?BEDFile   I'm not exactly sure what you mean by score of every chromosome, is that something that is provided in the file ...
written 5 weeks ago by shepherl ♦♦ 240
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Comment: C: strsplit method for DNAStringSet objects
... The DNAStringSet object sequences can be convert to a character vector to be used in strsplit.  For instance: library(ShortRead) sp <- SolexaPath(system.file('extdata', package='ShortRead')) rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt") strsplit(as.character(id(rfq)), split= ...
written 6 weeks ago by shepherl ♦♦ 240
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News: New Package Submission Deadline March 31
... The new package submission deadline is March 31. This deadline will serve as the potential to be included in release 3.5 pending review; packages after this deadline will remain in Bioconductor devel pending proper review.   ...
news bioconductor issue tracker written 9 weeks ago by shepherl ♦♦ 240

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Scholar 13 months ago, created an answer that has been accepted. For A: survcomp package - censor missing
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: survcomp package - censor missing

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