User: Valerie Obenchain

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Posts by Valerie Obenchain

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Answer: A: Error in VCF parsing with VariantAnnotation
... This question was also posted on github. Conversation has moved to https://github.com/Bioconductor/VariantAnnotation/issues/25. ...
written 3 months ago by Valerie Obenchain • 6.7k
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Comment: C: VariantAnnotation fails to load VCF record
... This conversation has moved to the github repo: https://github.com/Bioconductor/VariantAnnotation/issues/19 ...
written 5 months ago by Valerie Obenchain • 6.7k
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Answer: A: Bug in follow and precede
... Hi, There is a GRanges method for follow() so no need to call IRanges::follow(). By definition the IRanges method will ignore strand because IRanges objects do have have a strand. If you want to ignore strand in the GRanges, just use ignore.strand=TRUE. From the ?follow man page: • prece ...
written 6 months ago by Valerie Obenchain • 6.7k
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Answer: A: writeVcf save invalid vcf with metadata out of order
... Thanks for reporting the inconsistent ordering of the header lines in writeVcf(). I've checked in a fix to VariantAnnotation 1.28.2 and 1.29.1 to enforce 'fileformat' as the first line. As for the SAMPLE line in the header, this must be a carry over from your original file, e.g., header(scanVcfHe ...
written 6 months ago by Valerie Obenchain • 6.7k
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News: Bioconductor 3.8 is released
... Thanks to all developers and community members for contributing to the project! Please see the full release announcement here: https://www.bioconductor.org/news/bioc_3_8_release/ The Bioconductor Team ...
news bioconductor release written 7 months ago by Valerie Obenchain • 6.7k • updated 5 months ago by restat110 • 0
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Answer: A: Problem installing CRISPRseek
... Hi Louis, BiocInstaller is the name of the package and biocLite() is the function in the package that does the installing. It looks like you haven't called biocLite("CRISPRseek"). FYI, BiocInstaller::biocLite() is being phased out and replaced by BiocManager::install(): install.packages("BiocMan ...
written 8 months ago by Valerie Obenchain • 6.7k
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Comment: C: Trying to map nucleotide position from a transcript to genomic location
... Thank you. Now I understand what you're after. You need to use a different object as the 'transcripts' argument. In this case, "exons-by transcripts". snps <- GRanges("chr12", IRanges(1409, width=1)) tx_names <- c("uc007nhp.1", "uc007nhq.2") exbytx <- exonsBy(txdb, "tx", use.names=TRUE)[ ...
written 8 months ago by Valerie Obenchain • 6.7k
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Comment: C: Nearest genomic ranges and distances in circular ranges
... I've started a github issue for this: https://github.com/Bioconductor/GenomicRanges/issues/14 ...
written 8 months ago by Valerie Obenchain • 6.7k
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Answer: A: Data from ##SAMPLE lines in VCF?
... VariantAnnotation 1.27.6 and Rsamtools 1.33.6 have been updated to support VCFv4.3. I wanted to add some background to explain why we had the "META" DataFame in the first place. The meta-information lines in a VCF header are preceded by '##' and we can think of these key-value pairs as "simple" or ...
written 8 months ago by Valerie Obenchain • 6.7k
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Comment: C: Data from ##SAMPLE lines in VCF?
... Thanks for the report. The 'META' name clash is unfortunate. I'll work on a solution and should have something in they next couple of days. Valerie ...
written 8 months ago by Valerie Obenchain • 6.7k

Latest awards to Valerie Obenchain

Scholar 6 months ago, created an answer that has been accepted. For A: Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 13 months ago, created an answer that has been accepted. For A: Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
Popular Question 13 months ago, created a question with more than 1,000 views. For merging VCF files
Scholar 23 months ago, created an answer that has been accepted. For A: VariantAnnotation Installation Failure
Scholar 23 months ago, created an answer that has been accepted. For A: AnnotationHub: confusing pValue/qValue for (some) Roadmap records
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 23 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Popular Question 23 months ago, created a question with more than 1,000 views. For Bioconductor 3.5 is released
Popular Question 23 months ago, created a question with more than 1,000 views. For Bioconductor Package Archives
Appreciated 23 months ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Appreciated 23 months ago, created a post with more than 5 votes. For Bioconductor 3.7 is released
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Popular Question 23 months ago, created a question with more than 1,000 views. For merging VCF files
Popular Question 23 months ago, created a question with more than 1,000 views. For Integer overflow when summing an 'integer' Rle
Scholar 23 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: about collapsed and expanded vcf file
Scholar 2.0 years ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Appreciated 2.1 years ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Scholar 2.2 years ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Popular Question 2.3 years ago, created a question with more than 1,000 views. For merging VCF files
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 2.4 years ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
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