Admin: Valerie Obenchain

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Valerie Obenchain ♦♦ 6.2k
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Posts by Valerie Obenchain

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News: Bioconductor 3.6 release
... The release of Bioconductor 3.6 will be Tuesday, October 31. Please see the schedule for details:   http://www.bioconductor.org/developers/release-schedule/ Over the next month we'll announce key deadlines on the bioc-devel mailing list:   https://stat.ethz.ch/pipermail/bioc-devel/ Part of pre ...
news bioconductor release written 3 days ago by Valerie Obenchain ♦♦ 6.2k
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Comment: C: Error in columns(org.Hs.eg.db) : could not find function "columns"
... Please edit your question to show the error and the output of your sessionInfo(). ...
written 10 days ago by Valerie Obenchain ♦♦ 6.2k
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Answer: A: Not getting the expected answers from GenomicRanges follow/precede
... I agree this can be confusing. The behavior of precede() and follow() were established years ago and are documented in both IRanges and GRanges on ?precede or ?follow. These definitions are from the GenomicRanges package, those in IRanges are very similar:         • precede: For each range in ‘x’, ...
written 15 days ago by Valerie Obenchain ♦♦ 6.2k
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Answer: A: SNP location annotation problem in "VariantAnnotation" package
... The IntergenicVariants class has upstream and downstream values that define "how far" from the gene to search. Defaults are shown on the ?IntergenicVariants man page: IntergenicVariants(upstream = 1e+06L, downstream = 1e+06L, idType=c("gene", "tx")) If your SNP falls outside of these ranges it wo ...
written 15 days ago by Valerie Obenchain ♦♦ 6.2k
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Answer: A: Passing multiple arguments (like mapply) to the MAP-function in GenomicFiles.
... Unfortunately I don't think there is a straightforward way of doing this. There is no metadata per se associated with the files. Valerie ...
written 22 days ago by Valerie Obenchain ♦♦ 6.2k
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Comment: C: Translation Error in predictCoding() for VariantAnnotation
... I'm not sure why we see '**TTG**' for REFCODON - that's where the trouble starts. I can't try to reproduce this unless I know what annotation you used. Please edit your answer to include the annotation and the output of sessionInfo(). Valerie ...
written 24 days ago by Valerie Obenchain ♦♦ 6.2k
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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 4 weeks ago by Valerie Obenchain ♦♦ 6.2k
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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 5 weeks ago by Valerie Obenchain ♦♦ 6.2k
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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 7 weeks ago by Valerie Obenchain ♦♦ 6.2k
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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 12 weeks ago by Valerie Obenchain ♦♦ 6.2k

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Scholar 3 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Scholar 3 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Appreciated 5 months ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Scholar 5 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
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Popular Question 6 months ago, created a question with more than 1,000 views. For merging VCF files
Scholar 8 months ago, created an answer that has been accepted. 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
Scholar 17 months ago, created an answer that has been accepted. For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
Scholar 17 months ago, created an answer that has been accepted. For A: BiocParallel example does not work any more (sbatch produced exit code 1)
Scholar 17 months ago, created an answer that has been accepted. For A: Genomic features for genomic positions
Scholar 17 months ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Scholar 17 months ago, created an answer that has been accepted. For A: Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowP
Appreciated 17 months ago, created a post with more than 5 votes. For New Package Submission Process
Scholar 17 months ago, created an answer that has been accepted. For A: AnnotationHub: two broad peaks from same url are not the same
Scholar 17 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 17 months ago, created an answer that has been accepted. For A: GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Genomic features for genomic positions
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: readGAlignmentPairs slow in problematic region
Teacher 17 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 17 months ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 17 months ago, created an answer that has been accepted. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 17 months ago, created an answer that has been accepted. For A: Intersecting a Granges and a GRangesList using within
Scholar 18 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix

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