Admin: Valerie Obenchain

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Valerie Obenchain ♦♦ 5.9k
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Posts by Valerie Obenchain

<prev • 762 results • page 1 of 77 • next >
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News: Annotation packages maintained by Francesco Ferrari
... Hi, We have 24 annotation packages in the repo maintained by Francesco Ferrari, the majority of which are broken (output below). The last time these were updated was for Bioconductor 2.8 (3 years ago). We've tried a number of times to contact Francesco but did not get a response. The plan is to re ...
news written 8 days ago by Valerie Obenchain ♦♦ 5.9k
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Answer: A: How does the org.Dm.eg.db package deal with NOT annotation qualifiers when anno
... Thanks for the feedback. We're rebuilding the annotations over the next few weeks for the April 25 release and we won't include the GO terms with the NOT annotation. Valerie ...
written 8 days ago by Valerie Obenchain ♦♦ 5.9k
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Answer: A: Importing Gene Symbols with makeTxDbFromGFF
... The decision was made to not include a gene_name column in the TxDbs. This is explained on the ?transcripts man page: Finally, \code{use.names=TRUE} cannot be used when grouping by gene \code{by="gene"}. This is because, unlike for the other features, the gene ids are external ids (e.g ...
written 9 days ago by Valerie Obenchain ♦♦ 5.9k
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News: Bioconductor 3.5 release
... Hi all, The release of Bioconductor 3.5 will be Tuesday, April 25. 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. Lori sent the first one last week and it's important ...
news bioconductor release written 10 days ago by Valerie Obenchain ♦♦ 5.9k
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Answer: A: Troubles with new version of GenomicFeatures(?)
... I think it's related to a stale methods table as described here https://support.bioconductor.org/p/93347/. You could try re-installing GenomicFeatures and it's dependencies. FYI, when you post a question you should include the output from sessionInfo(). Valerie ...
written 15 days ago by Valerie Obenchain ♦♦ 5.9k
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Comment: C: error in installing bioconductor
... The biocLite() function is in the BiocInstaller package. Once BiocInstaller is installed you can either call library(BiocInstaller) in an R session or put library(BiocInstaller) in your .Rprofile to automatically load the package (which makes biocLite() available) when you start R. Valerie ...
written 15 days ago by Valerie Obenchain ♦♦ 5.9k
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Comment: C: BiocInstaller wants version of R that is not available yet
... Re-installing BiocInstaller will not help. You need to be using R devel (version >=3.4.0) to use these packages. Your R is 3.3.2. If you do upgrade to R 3.4.0, you need to (manually) install the data package before the software package; because these packages are not in the Bioconductor repo the ...
written 21 days ago by Valerie Obenchain ♦♦ 5.9k
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Comment: C: BiocInstaller wants version of R that is not available yet
... Maybe related ... I'm currently reviewing a package called TCGAWorkflow and the accompanying TCGAWorkflowData. They aren't approved yet so they aren't in the Bioconductor repos. Any installation of both packages would have to be (on your own) from the github repos. ...
written 21 days ago by Valerie Obenchain ♦♦ 5.9k
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Comment: C: goseq - supportedOrganisms error
... Oops, not related. Sorry for the misdiagnosis. Valerie ...
written 23 days ago by Valerie Obenchain ♦♦ 5.9k
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Comment: C: does readVcf mistakenly ignore ploidy for missing genotypes?
... Hi, Yes, readVcf() does currently ignore ploidy - all missing values are represented with a single '.' dot. This is a good suggestion and we'll make the change. There are several things before this on the TODO but we'll get to it as soon as we can. Valerie ...
written 24 days ago by Valerie Obenchain ♦♦ 5.9k

Latest awards to Valerie Obenchain

Teacher 15 days ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Popular Question 18 days ago, created a question with more than 1,000 views. For merging VCF files
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 9 weeks ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: readGAlignmentPairs slow in problematic region
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Genomic features for genomic positions
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: AnnotationHub: two broad peaks from same url are not the same
Appreciated 11 months ago, created a post with more than 5 votes. For New Package Submission Process
Scholar 11 months ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Scholar 11 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 11 months ago, created an answer that has been accepted. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 11 months ago, created an answer that has been accepted. For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
Scholar 11 months ago, created an answer that has been accepted. For A: AnnotationHub: two broad peaks from same url are not the same
Scholar 11 months ago, created an answer that has been accepted. For A: Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowP
Scholar 11 months ago, created an answer that has been accepted. For A: Genomic features for genomic positions
Scholar 11 months ago, created an answer that has been accepted. For A: GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Scholar 11 months ago, created an answer that has been accepted. For A: Intersecting a Granges and a GRangesList using within
Scholar 11 months ago, created an answer that has been accepted. For A: BiocParallel example does not work any more (sbatch produced exit code 1)
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 12 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Guru 12 months ago, received more than 100 upvotes.
Scholar 14 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 14 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Appreciated 14 months ago, created a post with more than 5 votes. For October Newsletter now available
Scholar 15 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix

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