Admin: Valerie Obenchain

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Valerie Obenchain ♦♦ 6.6k
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Posts by Valerie Obenchain

<prev • 825 results • page 1 of 83 • next >
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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 days ago by Valerie Obenchain ♦♦ 6.6k
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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 12 days ago by Valerie Obenchain ♦♦ 6.6k
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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 days ago by Valerie Obenchain ♦♦ 6.6k
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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 14 days ago by Valerie Obenchain ♦♦ 6.6k
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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 20 days ago by Valerie Obenchain ♦♦ 6.6k
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News: BioC 3.8 release schedule
... Hi all, The release of Bioconductor 3.8 will be on October 31:   https://www.bioconductor.org/developers/release-schedule/ Over the next weeks we'll announce key dates on the on bioc-devel@r-project.org mailing list. Thanks in advance for cleaning up packages and getting those last minute fixes ...
news bioconductor release written 22 days ago by Valerie Obenchain ♦♦ 6.6k
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Answer: A: Trying to map nucleotide position from a transcript to genomic location
... Hi Vicky, I'm not sure why you think the results from mapFromTranscripts() are incorrect. I've used "Bcap29" as an example - Set up: snps <- GRanges("Bcap29", IRanges(1409, width=1)) library(org.Mm.eg.db) geneid <- select(org.Mm.eg.db, "Bcap29", "ENTREZID", "SYMBOL") txdb <- TxDb.Mmuscu ...
written 28 days ago by Valerie Obenchain ♦♦ 6.6k
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Comment: C: getPromoterSeq error "Error in value[[3L]](cond) : record 1 (1:-XXXX-XXX) was t
... Please update to a current version of R/Bioconductor (release is R 3.5 / Bioc 3.7). See this page for help: https://www.bioconductor.org/install/ If you still see the error after updating, post back and show your sessionInfo() again. Likely the error is triggered by specific ranges in myGranges. I ...
written 6 weeks ago by Valerie Obenchain ♦♦ 6.6k
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Comment: C: Nearest genomic ranges and distances in circular ranges
... Hi, We've discussed this and it's not entirely clear what precede and follow mean for circular chromosomes. Should chromosome length be interpreted as the stop point in this case? For example, the current precede, follow have a select=c("first", "all") argument. What would be returned when select=a ...
written 8 weeks ago by Valerie Obenchain ♦♦ 6.6k
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Comment: C: ExperimentHub wackiness (which breaks packages that depend upon experimentHub-pr
... FYI this does not look related to the server updates I mentioned in response to this thread: https://stat.ethz.ch/pipermail/bioc-devel/2018-August/013896.html. I don't think my response has posted to bioc-devel yet but I wanted to close the loop here. Valerie ...
written 9 weeks ago by Valerie Obenchain ♦♦ 6.6k

Latest awards to Valerie Obenchain

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 5 months ago, created an answer that has been accepted. For A: Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
Popular Question 5 months ago, created a question with more than 1,000 views. For merging VCF files
Scholar 15 months ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Teacher 15 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: VariantAnnotation Installation Failure
Popular Question 15 months ago, created a question with more than 1,000 views. For Bioconductor 3.5 is released
Appreciated 15 months ago, created a post with more than 5 votes. For Bioconductor 3.7 is released
Scholar 15 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Popular Question 15 months ago, created a question with more than 1,000 views. For Bioconductor Package Archives
Appreciated 15 months ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Popular Question 15 months ago, created a question with more than 1,000 views. For Integer overflow when summing an 'integer' Rle
Scholar 15 months ago, created an answer that has been accepted. For A: AnnotationHub: confusing pValue/qValue for (some) Roadmap records
Popular Question 15 months ago, created a question with more than 1,000 views. For merging VCF files
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 16 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Scholar 16 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Appreciated 17 months ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Scholar 18 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Popular Question 19 months ago, created a question with more than 1,000 views. For merging VCF files
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 21 months 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: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage

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