Admin: Valerie Obenchain

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Valerie Obenchain ♦♦ 6.4k
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Posts by Valerie Obenchain

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Answer: A: How to operate on circular sequences with GenomicRanges?
... Hi, The ?GNCList man page in GenomicRanges has examples of overlaps with circular sequences. See the "With Circular Sequences" section at the bottom. The range to overlap should extend past the end of the circular sequence, not start again at '1'. In your example above the range would start at 165 ...
written 10 hours ago by Valerie Obenchain ♦♦ 6.4k
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Answer: A: Minimum overlap for reads to be counted in summarizeoverlaps
... That's a pretty thorough discussion on the page you reference. In one of the responses I specify that overlap only requires one base. Are you also using bedtools? Are you seeing some kind of inconsistency? It would be good to see a code example if you have a specific question. Valerie   Edit: Spe ...
written 1 day ago by Valerie Obenchain ♦♦ 6.4k
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Answer: A: GRanges::distanceToNearest does not return distance to nearest
... Hi, Thanks for your patience. This is now fixed in GenomicRanges 1.31.3 in devel and 1.30.1 in release. Both should be available via biocLite() tomorrow around 3pm EST. The bug was hitting the case where a '*' query followed both a '+' and '-' range in subject. Instead of choosing the closest rang ...
written 9 weeks ago by Valerie Obenchain ♦♦ 6.4k
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Answer: A: [VariantAnnotation] Preserve query metadata with locateVariants()
... Hi, The result of locateVariants() is a "reped out" GRanges; one row for each variant-transcript match. To add the query metadata to the result you could rep out the metadata in the query using the 'QUERYID' column from the result. From the man page, ‘QUERYID’ The ‘QUERYID’ column provides a ...
written 9 weeks ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: GRanges::distanceToNearest does not return distance to nearest
... Thanks for reporting this bug. We'll post back when it's fixed. Valerie ...
written 10 weeks ago by Valerie Obenchain ♦♦ 6.4k
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Answer: A: Issues installing "CardinalWorkflows"
... Looks like a problem with the space in 'Program Files' in the path. You need quotes around this - either when defined as a variable or invoked. If that doesn't work, try using a library path (see ?.libPaths() or ?R_LIBS_USER) that does not contain spaces or special characters. Valerie ...
written 11 weeks ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: 403 Forbidden During Install
... Thanks for sending the IP and yes, it was blacked for the reasons you describe. It's been removed from the blacklist and you should have access now. Thanks for fixing the cluster configuration. Valerie ...
written 3 months ago by Valerie Obenchain ♦♦ 6.4k
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Answer: A: 403 Forbidden During Install
... What is the IP of the cluster being blocked? Valerie ...
written 3 months ago by Valerie Obenchain ♦♦ 6.4k
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News: Bioconductor Package Archives
... BioC community, Starting with BioC 3.6 we are providing an Archive directory for each release. The Archive contains all package versions that occur during the 6 month cycle. This will be done for the release branch only. The structure is similar to the CRAN Archives except there will be a separate ...
news bioconductor archive written 3 months ago by Valerie Obenchain ♦♦ 6.4k
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News: Bioconductor 3.6 is released
... Thanks to all the developers for your contribution to the project! Full release announcement here:   http://bioconductor.org/news/bioc_3_6_release/ ...
news bioconductor release written 3 months ago by Valerie Obenchain ♦♦ 6.4k

Latest awards to Valerie Obenchain

Scholar 8 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Scholar 8 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Appreciated 10 months ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Scholar 10 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Popular Question 11 months ago, created a question with more than 1,000 views. For merging VCF files
Scholar 13 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 22 months ago, created an answer that has been accepted. For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
Scholar 22 months ago, created an answer that has been accepted. For A: BiocParallel example does not work any more (sbatch produced exit code 1)
Scholar 22 months ago, created an answer that has been accepted. For A: Genomic features for genomic positions
Scholar 22 months ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Scholar 22 months ago, created an answer that has been accepted. For A: Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowP
Appreciated 22 months ago, created a post with more than 5 votes. For New Package Submission Process
Scholar 22 months ago, created an answer that has been accepted. For A: AnnotationHub: two broad peaks from same url are not the same
Scholar 22 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 22 months ago, created an answer that has been accepted. For A: GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Genomic features for genomic positions
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: readGAlignmentPairs slow in problematic region
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: AnnotationHub: two broad peaks from same url are not the same
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 22 months ago, created an answer that has been accepted. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 22 months ago, created an answer that has been accepted. For A: Intersecting a Granges and a GRangesList using within
Scholar 23 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix

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