Admin: Valerie Obenchain

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Valerie Obenchain ♦♦ 5.8k
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Posts by Valerie Obenchain

<prev • 743 results • page 1 of 75 • next >
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Answer: A: genomicAlignments: fail to run readGAlignments example code
... I cannot reproduce this error. Are you still having this problem? Valerie ...
written 8 hours ago by Valerie Obenchain ♦♦ 5.8k
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Comment: C: `precede` does not perform as expected
... After some discussion, the following changes were made to precede() and follow() in GenomicRanges 1.27.21: 1) The 'select' argument has been made consistent with the methods in IRanges: precede() now supports select=c("first", "all") and follow() supports select=c("last", "all"). 2) When 'x' is '* ...
written 2 days ago by Valerie Obenchain ♦♦ 5.8k
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Comment: C: about collapsed and expanded vcf file
... The ExpandedVCF class is a flat-ish form of the CollapsedVCF. The expansion is centered around the ALT field. Often there can be more than one ALT value per variant and in the CollapsedVCF all ALT values for a single variant are presented in a single row. While there is one row per genomic position, ...
written 9 days ago by Valerie Obenchain ♦♦ 5.8k
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Answer: A: about collapsed and expanded vcf file
... The ?VCF man page explains the difference between Collapsed and Expanded VCF classes. Both extend the VCF class (use showClass("CollapsedVCF")) so methods set on the VCF class are inherited by both. To see what classes a method operates on use showMethods(), e.g.,  > showMethods("alt") Functio ...
written 10 days ago by Valerie Obenchain ♦♦ 5.8k
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Comment: C: `precede` does not perform as expected
... Thanks for the small, concise example. You're right, "*" strand is treating all ranges as if on the "+" strand. Here is my svn commit from 2015 confirming it: ------------------------------------------------------------------------ r108978 | v.obenchain | 2015-09-29 14:56:24 -0700 (Tue, 29 Sep 2015 ...
written 17 days ago by Valerie Obenchain ♦♦ 5.8k
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Answer: A: `precede` does not perform as expected
... Hi Can, As you can imagine, people have different opinions on 'right behavior' of a function. precede() and follow() handle strand the way they do because of user input at the time they were written. It sounds like you want to make specific strand comparisons in a certain order. Instead of modifyi ...
written 19 days ago by Valerie Obenchain ♦♦ 5.8k
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Comment: C: Problem with AnnotationHub()
... Several of us have tested and can't reproduce the problem. From the command line (not in R): ~/sandbox >curl -I https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3 HTTP/1.1 200 OK Date: Thu, 29 Dec 2016 16:00:09 GMT Server: Apache/2.4.9 (Ubuntu) X-Content-Type-Options: nosniff ...
written 20 days ago by Valerie Obenchain ♦♦ 5.8k
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Comment: C: Problem with AnnotationHub()
... No, that post is very old and the issues have been addressed. The 'cache' is the .AnnotationHub/ directory with the sqlite file, index file and individual downloaded resources. If you removed the .AnnotationHub directory you removed the cache. I don't know why you're having problems with the SSL CA ...
written 20 days ago by Valerie Obenchain ♦♦ 5.8k
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Comment: C: Problem with AnnotationHub()
... OK, those package versions now look like Bioconductor 3.4. I would exit R and then remove the .AnnotationHub directory. The directory will be in your local home so for example to remove mine I would  rm -r /home/vobencha/.AnnotationHub Once you've confirmed there is no .AnnotationHub, start R and ...
written 20 days ago by Valerie Obenchain ♦♦ 5.8k
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Answer: A: Problem with AnnotationHub()
... Hi, It looks like you are a release behind and need to update R/Bioconductor. The current release version of Biocondcutor is 3.4 (AnnotationHub package version 2.6.*). Update instructions are here: http://www.bioconductor.org/install/ Let us know if you still have the problem after the update. V ...
written 21 days ago by Valerie Obenchain ♦♦ 5.8k

Latest awards to Valerie Obenchain

Scholar 10 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Guru 10 months ago, received more than 100 upvotes.
Scholar 12 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 12 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Appreciated 12 months ago, created a post with more than 5 votes. For October Newsletter now available
Scholar 13 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 14 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 14 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 14 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: readGAlignmentPairs slow in problematic region
Scholar 15 months ago, created an answer that has been accepted. For A: Intersecting a Granges and a GRangesList using within
Scholar 15 months ago, created an answer that has been accepted. For A: Rsamtools and dbnsfp
Scholar 18 months ago, created an answer that has been accepted. For A: Rsamtools and dbnsfp
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Does the BAM need to be sorted by name for "summarizeOverlaps" of "GenomicAlignm
Scholar 18 months ago, created an answer that has been accepted. For A: Rsamtools and dbnsfp
Scholar 18 months ago, created an answer that has been accepted. For A: Rsamtools and dbnsfp
Scholar 20 months ago, created an answer that has been accepted. For A: Metadata Missing from vcf when reading in with readVcfAsVRanges
Scholar 23 months ago, created an answer that has been accepted. For A: Metadata Missing from vcf when reading in with readVcfAsVRanges
Scholar 23 months ago, created an answer that has been accepted. For A: promoter definition in VariantAnnotation
Scholar 23 months ago, created an answer that has been accepted. For A: promoter definition in VariantAnnotation
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics researching Schizophrenia
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Bioinformatics researching Schizophrenia
Scholar 2.0 years ago, created an answer that has been accepted. For A: promoter definition in VariantAnnotation
Scholar 2.0 years ago, created an answer that has been accepted. For A: writeVcf no longer writes records for ungenotyped data
Scholar 2.2 years ago, created an answer that has been accepted. For A: writeVcf no longer writes records for ungenotyped data

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