Admin: Valerie Obenchain

gravatar for Valerie Obenchain
Valerie Obenchain ♦♦ 6.1k
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Posts by Valerie Obenchain

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Comment: C: Bioconductor 3.5 is released
... Updated the post with a few changes to  the 'Deprecated and Defunct Packages'. section. Valerie ...
written 28 days ago by Valerie Obenchain ♦♦ 6.1k
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News: Bioconductor 3.5 is released
... April 25, 2017 Bioconductors: We are pleased to announce Bioconductor 3.5, consisting of 1383 software packages, 316 experiment data packages, and 911 annotation packages. There are 88 new software packages, and many updates and improvements to existing packages; Bioconductor 3.5 is compatible wi ...
news bioconductor release written 29 days ago by Valerie Obenchain ♦♦ 6.1k • updated 25 days ago by Hervé Pagès ♦♦ 12k
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Comment: C: What are out-of-bound ranges? Is it necessary to get rid of them?
... Please tag your message with the package name, ChIPpeakAnno, so the author is aware of the question. ...
written 5 weeks ago by Valerie Obenchain ♦♦ 6.1k • updated 5 weeks ago by Martin Morgan ♦♦ 19k
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Comment: C: AnnotationHub-cant extract database
... The problem is with the version of AnnotationHub - it's 2 (soon to be 3 ) releases old. The current release is version 2.6.5 seen here: http://www.bioconductor.org/checkResults/release/bioc-LATEST/ The old 2.4.2 version does not have the correct logic implemented for the OrgDb objects. The data in ...
written 5 weeks ago by Valerie Obenchain ♦♦ 6.1k
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Answer: A: AnnotationHub-cant extract database
... Hi, Your sessionInfo() looks good. I see you're using the current release (Bioconductor 3.4) and have the current version of AnnotationHub loaded. Bioconductor 3.4 was released in October 2016 that is why when you load AnnotationHub the default snapshot date is 2016-10-11: > hub = AnnotationHub ...
written 6 weeks ago by Valerie Obenchain ♦♦ 6.1k
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Comment: C: AnnotationHub-cant extract database
... Cut and paste error? Not sure what happened but it would be good to see the output of sessionInfo() from your coworker. ...
written 6 weeks ago by Valerie Obenchain ♦♦ 6.1k
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Comment: C: AnnotationHub-cant extract database
... We need to see the output of sessionInfo() for both you and your coworker. This will show the R/Bioconductor package versions you're using. For example, here is mine - > sessionInfo() R Under development (unstable) (2017-03-15 r72352) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Fedora ...
written 6 weeks ago by Valerie Obenchain ♦♦ 6.1k
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Comment: C: AnnotationHub-cant extract database
... Please show the exact commands you and your coworker are running and include the output from sessionInfo(). It does not matter if you are on windows, linux or mac; what will matter is the version of R/Bioconductor you are using. Valerie ...
written 6 weeks ago by Valerie Obenchain ♦♦ 6.1k
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Comment: C: How does the org.Dm.eg.db package deal with NOT annotation qualifiers when anno
... Hi, I've just finished building the new db0 packages (versions 3.4.2). It turns out that we do filter out genes with the NOT qualifier ... the catch is that some of these genes have a gene ID -> GO mapping that is both ok and a NOT. The output below is from an intermediate database used to build ...
written 7 weeks ago by Valerie Obenchain ♦♦ 6.1k
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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 9 weeks ago by Valerie Obenchain ♦♦ 6.1k

Latest awards to Valerie Obenchain

Appreciated 28 days ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 5 weeks ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Popular Question 10 weeks ago, created a question with more than 1,000 views. For merging VCF files
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 4 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Scholar 13 months ago, created an answer that has been accepted. For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
Scholar 13 months ago, created an answer that has been accepted. For A: BiocParallel example does not work any more (sbatch produced exit code 1)
Scholar 13 months ago, created an answer that has been accepted. For A: Genomic features for genomic positions
Scholar 13 months ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Scholar 13 months ago, created an answer that has been accepted. For A: Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowP
Appreciated 13 months ago, created a post with more than 5 votes. For New Package Submission Process
Scholar 13 months ago, created an answer that has been accepted. For A: AnnotationHub: two broad peaks from same url are not the same
Scholar 13 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Scholar 13 months ago, created an answer that has been accepted. For A: GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Scholar 13 months ago, created an answer that has been accepted. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 13 months ago, created an answer that has been accepted. For A: Intersecting a Granges and a GRangesList using within
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Genomic features for genomic positions
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: readGAlignmentPairs slow in problematic region
Teacher 13 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 13 months ago, created an answer with at least 3 up-votes. For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar 14 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix
Guru 14 months ago, received more than 100 upvotes.
Scholar 16 months ago, created an answer that has been accepted. For A: inconsistent default of file suffix

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