Admin: Valerie Obenchain

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Valerie Obenchain ♦♦ 6.2k
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Posts by Valerie Obenchain

<prev • 777 results • page 1 of 78 • next >
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Answer: A: SNPs in multiple locations
... Hi, On the locateVariants man page it says this under the 'Value' section:      A ‘GRanges’ object with a row for each variant-transcript match. This means a single SNP may be classified as more than one feature and each feature is returned as a separate row. For your example it sounds like the S ...
written 27 days ago by Valerie Obenchain ♦♦ 6.2k
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Answer: A: summarizeVariants from VariantAnnotation reordering genes in rownames
... Hi, I think results in rowRanges() and assays()$counts are consistent. The show method for RangedSummarizedExperiment displays the column names for assays()$counts instead of the row names and maybe that's the point of confusion. The contract for the class is that the rows of rowRanges() match the ...
written 4 weeks ago by Valerie Obenchain ♦♦ 6.2k
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Answer: A: Error in GenomeInfoDb:::getDanglingSeqlevels
... The seqlevel() setter was modified last year to include a pruning.mode argument. The error message shows the code necessary to drop seqlevels in using  this argument. This is documented, with examples, on the ?seqlevels man page. If you are seeing this error from running a function in ggbio and not ...
written 4 weeks ago by Valerie Obenchain ♦♦ 6.2k
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Answer: A: No annotation for single SNPs
... Hi, Yes, this is a bug. * locateVariants(query, subject, region=AllVariants()) should return all 8 variant types described on the ?AllVariants man page * 'upstream' and 'downstream' parameters in AllVariants() can be set for both PromoterVariants() and IntergenicVariants() but not IntronVariants( ...
written 5 weeks ago by Valerie Obenchain ♦♦ 6.2k
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Comment: C: VariantAnnotation Installation Failure
... I'm not an RStudio expert but yes, I would think restarting R within RStudio should delete the tmp/. If you restarted R and still got the error it sounds like a problem on our end with the caching. I'll look into this further. Valerie ...
written 8 weeks ago by Valerie Obenchain ♦♦ 6.2k
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Answer: A: VariantAnnotation Installation Failure
... Hi Andrew, The issue you're seeing is related to a stale PACKAGES file. This file lists package versions - if it's stale then the version will not match that in the repository (e.g., trying to retrieve VariantAnnotation 1.22.0 when the package had moved on to 1.22.1 or greater). There are a couple ...
written 8 weeks ago by Valerie Obenchain ♦♦ 6.2k
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Comment: C: Bioconductor 3.5 is released
... Updated the post with a few changes to  the 'Deprecated and Defunct Packages'. section. Valerie ...
written 3 months ago by Valerie Obenchain ♦♦ 6.2k
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News: Bioconductor 3.5 is released
... April 25, 2017 Bioconductors: We are pleased to announce Bioconductor 3.5, consisting of 1383 software packages, 316 experiment data packages, and 911 annotation packages. There are 88 new software packages, and many updates and improvements to existing packages; Bioconductor 3.5 is compatible wi ...
news bioconductor release written 3 months ago by Valerie Obenchain ♦♦ 6.2k • updated 12 weeks ago by Hervé Pagès ♦♦ 12k
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Comment: C: What are out-of-bound ranges? Is it necessary to get rid of them?
... Please tag your message with the package name, ChIPpeakAnno, so the author is aware of the question. ...
written 3 months ago by Valerie Obenchain ♦♦ 6.2k • updated 3 months ago by Martin Morgan ♦♦ 20k
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Comment: C: AnnotationHub-cant extract database
... The problem is with the version of AnnotationHub - it's 2 (soon to be 3 ) releases old. The current release is version 2.6.5 seen here: http://www.bioconductor.org/checkResults/release/bioc-LATEST/ The old 2.4.2 version does not have the correct logic implemented for the OrgDb objects. The data in ...
written 3 months ago by Valerie Obenchain ♦♦ 6.2k

Latest awards to Valerie Obenchain

Scholar 5 weeks ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Scholar 8 weeks ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Appreciated 3 months ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Scholar 3 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Popular Question 4 months ago, created a question with more than 1,000 views. For merging VCF files
Scholar 6 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 15 months ago, created an answer that has been accepted. For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
Scholar 15 months ago, created an answer that has been accepted. For A: BiocParallel example does not work any more (sbatch produced exit code 1)
Scholar 15 months ago, created an answer that has been accepted. For A: Genomic features for genomic positions
Scholar 15 months ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Scholar 15 months ago, created an answer that has been accepted. For A: Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowP
Appreciated 15 months ago, created a post with more than 5 votes. For New Package Submission Process
Scholar 15 months ago, created an answer that has been accepted. For A: AnnotationHub: two broad peaks from same url are not the same
Scholar 15 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 15 months ago, created an answer that has been accepted. For A: GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Genomic features for genomic positions
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: readGAlignmentPairs slow in problematic region
Teacher 15 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 15 months ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 15 months ago, created an answer that has been accepted. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 15 months ago, created an answer that has been accepted. For A: Intersecting a Granges and a GRangesList using within
Scholar 16 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix

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