User: Valerie Obenchain

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Posts by Valerie Obenchain

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Answer: A: Should GenomicAlignments::mapToAlignments() terminate when no alignments are fou
... This is fixed in GenomicAlignments 1.22.1 and 1.23.1. Valerie ...
written 23 days ago by Valerie Obenchain6.7k
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Comment: C: Should GenomicAlignments::mapToAlignments() terminate when it no alignments are
... Hi Shian, Thanks for the report and clear example. I'll look into it. Valerie ...
written 25 days ago by Valerie Obenchain6.7k
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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 8 months ago by Valerie Obenchain6.7k
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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 10 months ago by Valerie Obenchain6.7k
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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 12 months ago by Valerie Obenchain6.7k
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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 12 months ago by Valerie Obenchain6.7k
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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 13 months ago by Valerie Obenchain6.7k • updated 11 months ago by restat1100
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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 14 months ago by Valerie Obenchain6.7k
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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 14 months ago by Valerie Obenchain6.7k
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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 14 months ago by Valerie Obenchain6.7k

Latest awards to Valerie Obenchain

Scholar 12 months ago, created an answer that has been accepted. For A: Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 18 months ago, created an answer that has been accepted. For A: Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
Popular Question 19 months ago, created a question with more than 1,000 views. For merging VCF files
Scholar 2.4 years ago, created an answer that has been accepted. For A: VariantAnnotation Installation Failure
Scholar 2.4 years ago, created an answer that has been accepted. For A: AnnotationHub: confusing pValue/qValue for (some) Roadmap records
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
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Bioconductor 3.5 is released
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Bioconductor Package Archives
Appreciated 2.4 years ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Appreciated 2.4 years ago, created a post with more than 5 votes. For Bioconductor 3.7 is released
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Popular Question 2.4 years ago, created a question with more than 1,000 views. For merging VCF files
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Integer overflow when summing an 'integer' Rle
Scholar 2.4 years ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Scholar 2.5 years ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Scholar 2.5 years ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Appreciated 2.6 years ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Scholar 2.6 years ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Popular Question 2.7 years ago, created a question with more than 1,000 views. For merging VCF files
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 2.9 years ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file

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