Admin: Valerie Obenchain

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Valerie Obenchain ♦♦ 6.4k
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Posts by Valerie Obenchain

<prev • 790 results • page 2 of 79 • next >
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Answer: A: Can I ask questions on packages from CRAN?
... It's better to ask on one of the R / CRAN mailing lists: https://www.r-project.org/mail.html Valerie ...
written 12 weeks ago by Valerie Obenchain ♦♦ 6.4k
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Answer: A: locateVariants function does not find an annotation for the locus
... Hi, locateVariants() identifies hits in regions more specific than the at level of gene or transcript. Regions are documented on the ?AllVariants man page and are either parts of a gene or regions surrounding a gene. CodingVariants() IntronVariants() FiveUTRVariants() ThreeUTRVariants() SpliceSit ...
written 3 months ago by Valerie Obenchain ♦♦ 6.4k
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Answer: A: VariantAnnotation: Error with ScanVcfParam
... The error says the tabix file doesn't have a chromosome named 'chr5'. Is this true? Have you checked the file to see how the chromosome names are represented? Depending on how the file was generated it might have just '5' with no 'chr' prefix or maybe there isn't any chromosome 5 data in there. Val ...
written 3 months ago by Valerie Obenchain ♦♦ 6.4k
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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 4 months ago by Valerie Obenchain ♦♦ 6.4k
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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 months ago by Valerie Obenchain ♦♦ 6.4k
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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 months ago by Valerie Obenchain ♦♦ 6.4k
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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 4 months ago by Valerie Obenchain ♦♦ 6.4k
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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 5 months ago by Valerie Obenchain ♦♦ 6.4k
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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 5 months ago by Valerie Obenchain ♦♦ 6.4k
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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 6 months ago by Valerie Obenchain ♦♦ 6.4k

Latest awards to Valerie Obenchain

Scholar 4 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Scholar 5 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Appreciated 6 months ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Scholar 7 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Popular Question 8 months ago, created a question with more than 1,000 views. For merging VCF files
Scholar 9 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 19 months ago, created an answer that has been accepted. For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
Scholar 19 months ago, created an answer that has been accepted. For A: BiocParallel example does not work any more (sbatch produced exit code 1)
Scholar 19 months ago, created an answer that has been accepted. For A: Genomic features for genomic positions
Scholar 19 months ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Scholar 19 months ago, created an answer that has been accepted. For A: Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowP
Appreciated 19 months ago, created a post with more than 5 votes. For New Package Submission Process
Scholar 19 months ago, created an answer that has been accepted. For A: AnnotationHub: two broad peaks from same url are not the same
Scholar 19 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 19 months ago, created an answer that has been accepted. For A: GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Genomic features for genomic positions
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: readGAlignmentPairs slow in problematic region
Teacher 19 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 19 months ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 19 months ago, created an answer that has been accepted. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 19 months ago, created an answer that has been accepted. For A: Intersecting a Granges and a GRangesList using within
Scholar 20 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix

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