Admin: Valerie Obenchain

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Valerie Obenchain ♦♦ 6.4k
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Posts by Valerie Obenchain

<prev • 804 results • page 1 of 81 • next >
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Answer: A: counting reads with muliple hits with SummarizeOverlaps
... Hi, I think your question is why is there a count for Union when a read overlaps with multiple ranges in a single element of a GRangesList. That's the question I'll answer - if that's wrong, please clarify. An element of a GRangesList is considered a single feature. If a read overlaps with any of ...
written 9 days ago by Valerie Obenchain ♦♦ 6.4k
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Answer: A: How to write a preprocess.reads function for summarizeOverlaps that requires dif
... If you're calling summarizedOverlaps with the reads in a GAlignmentsPairs then yes, this would be the way to go. If instead the reads are in a BAM file they will be read into different classes depending on the value of the fragments argument. When you provide a BAM file of paired-end reads with fra ...
written 11 days ago by Valerie Obenchain ♦♦ 6.4k
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Answer: A: GenomicRanges distanceToNearest: trouble replicating snp-gene mapping from older
... Hi Shraddha, It's best to use the most current package versions as they will contain bug fixes. A bug was identified in distanceToNearest() a few months ago and has been fixed in the release and devel branches. To see what version a package is at in release and devel check the build report: https: ...
written 11 days ago by Valerie Obenchain ♦♦ 6.4k
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News: Bioconductor 3.7 release schedule
... Developers and Community Members, The release of Bioconductor 3.7 will be on Tuesday, May 1, 2018. Please see the schedule for details: https://www.bioconductor.org/developers/release-schedule/ Over the next month key deadlines will be announced on the bioc-devel mailing list: https://stat.ethz. ...
news bioconductor release written 29 days ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: GenomicFeatures: could not find symbol "recursive" in environment of the generic
... Sounds like you may have out of date packages. Please run BiocInstaller::biocValid(), update old packages and let us know if the error persists. Valerie ...
written 4 weeks ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: Error in installation of Bioconductor package
... Are you still having this problem? After you source("https://bioconductor.org/biocLite.R") what happens when you call library(BiocInstaller) Valerie ...
written 8 weeks ago by Valerie Obenchain ♦♦ 6.4k
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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 8 weeks 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 9 weeks 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 4 months 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 4 months ago by Valerie Obenchain ♦♦ 6.4k

Latest awards to Valerie Obenchain

Scholar 10 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Scholar 11 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Appreciated 12 months ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Scholar 12 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 12 months ago, created an answer with at least 3 up-votes. 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
Popular Question 13 months ago, created a question with more than 1,000 views. For merging VCF files
Scholar 15 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 24 months ago, created an answer that has been accepted. For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
Scholar 24 months ago, created an answer that has been accepted. For A: BiocParallel example does not work any more (sbatch produced exit code 1)
Scholar 24 months ago, created an answer that has been accepted. For A: Genomic features for genomic positions
Scholar 24 months ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Scholar 24 months ago, created an answer that has been accepted. For A: Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowP
Appreciated 24 months ago, created a post with more than 5 votes. For New Package Submission Process
Scholar 24 months ago, created an answer that has been accepted. For A: AnnotationHub: two broad peaks from same url are not the same
Scholar 24 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 24 months ago, created an answer that has been accepted. For A: GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Genomic features for genomic positions
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: readGAlignmentPairs slow in problematic region
Teacher 24 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 24 months ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 24 months ago, created an answer that has been accepted. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 24 months ago, created an answer that has been accepted. For A: Intersecting a Granges and a GRangesList using within
Scholar 2.1 years ago, created an answer that has been accepted. For A: inconsistent default of file suffix

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