Admin: Valerie Obenchain

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Valerie Obenchain ♦♦ 6.5k
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Posts by Valerie Obenchain

<prev • 809 results • page 1 of 81 • next >
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Answer: A: cram for new chips
... Hi, Yes, you can provide your own annotation package for this chip. I'm not familiar with these data but with some help from a colleague (thanks Jim!) it sounds like they're similar to the infinium chip packages https://www.bioconductor.org/packages/release/data/annotation/html/FDb.InfiniumMethyla ...
written 7 hours ago by Valerie Obenchain ♦♦ 6.5k
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Answer: A: Error with R package motifbreakR while trying to read a vcf file with snps.from.
... Hi, elementLengths() was deprecated some time ago (2016 I think) and replaced with elementNROWS(). The generic is in the S4Vectors package. The current Bioconductor release and devel use R 3.5. S4Vectors is at version 0.18.3 in release and 0.19.14, you can see the most current versions on the buil ...
written 3 days ago by Valerie Obenchain ♦♦ 6.5k
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Answer: A: filtering a VCF file based on genotype
... You can use filterVcf to remove rows from a vcf file that meet certain criteria. (The function does not filter by sample/column.) From the ?filterVcf man page: There are up to two passes. In the first pass, unparsed lines are passed to \code{prefilters} for filtering, e.g., searching for a fixed c ...
written 5 weeks ago by Valerie Obenchain ♦♦ 6.5k
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News: Bioconductor 3.7 is released
... Thanks to all developers and community members for contributing to the project! Full release announcement here:   http://bioconductor.org/news/bioc_3_7_release/   The Bioconductor Team ...
news bioconductor release written 7 weeks ago by Valerie Obenchain ♦♦ 6.5k • updated 7 weeks ago by funnyjokes1.com0
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Comment: C: Bioconductor Cloud AMI - How to Access Microarray Files Stored in Amazon S3 Buck
... The location of a file in a AWS S3 bucket is defined by a url. To download the file, you can use this url in an function that supports remote downloads, e.g., `download.file()`.  I'm not familiar with the functions in oligo so I'm not sure if they offer a function that downloads remote CEL files an ...
written 8 weeks ago by Valerie Obenchain ♦♦ 6.5k
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Answer: A: counting reads with muliple hits with SummarizeOverlaps
... Hi, I think your question is why is there a count for Union when a read overlaps with multiple ranges in a single element of a GRangesList. That's the question I'll answer - if that's wrong, please clarify. An element of a GRangesList is considered a single feature. If a read overlaps with any of ...
written 9 weeks ago by Valerie Obenchain ♦♦ 6.5k
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Answer: A: How to write a preprocess.reads function for summarizeOverlaps that requires dif
... If you're calling summarizedOverlaps with the reads in a GAlignmentsPairs then yes, this would be the way to go. If instead the reads are in a BAM file they will be read into different classes depending on the value of the fragments argument. When you provide a BAM file of paired-end reads with fra ...
written 10 weeks ago by Valerie Obenchain ♦♦ 6.5k
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Answer: A: GenomicRanges distanceToNearest: trouble replicating snp-gene mapping from older
... Hi Shraddha, It's best to use the most current package versions as they will contain bug fixes. A bug was identified in distanceToNearest() a few months ago and has been fixed in the release and devel branches. To see what version a package is at in release and devel check the build report: https: ...
written 10 weeks ago by Valerie Obenchain ♦♦ 6.5k
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News: Bioconductor 3.7 release schedule
... Developers and Community Members, The release of Bioconductor 3.7 will be on Tuesday, May 1, 2018. Please see the schedule for details: https://www.bioconductor.org/developers/release-schedule/ Over the next month key deadlines will be announced on the bioc-devel mailing list: https://stat.ethz. ...
news bioconductor release written 12 weeks ago by Valerie Obenchain ♦♦ 6.5k
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Comment: C: GenomicFeatures: could not find symbol "recursive" in environment of the generic
... Sounds like you may have out of date packages. Please run BiocInstaller::biocValid(), update old packages and let us know if the error persists. Valerie ...
written 3 months ago by Valerie Obenchain ♦♦ 6.5k

Latest awards to Valerie Obenchain

Popular Question 5 weeks ago, created a question with more than 1,000 views. For merging VCF files
Teacher 12 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: VariantAnnotation Installation Failure
Popular Question 12 months ago, created a question with more than 1,000 views. For Bioconductor 3.5 is released
Scholar 12 months ago, created an answer that has been accepted. For A: AnnotationHub: confusing pValue/qValue for (some) Roadmap records
Scholar 12 months ago, created an answer that has been accepted. For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Appreciated 12 months ago, created a post with more than 5 votes. For Bioconductor 3.7 is released
Scholar 12 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Popular Question 12 months ago, created a question with more than 1,000 views. For Bioconductor Package Archives
Popular Question 12 months ago, created a question with more than 1,000 views. For merging VCF files
Appreciated 12 months ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Popular Question 12 months ago, created a question with more than 1,000 views. For Integer overflow when summing an 'integer' Rle
Scholar 12 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: about collapsed and expanded vcf file
Appreciated 14 months ago, created a post with more than 5 votes. For Bioconductor 3.5 is released
Scholar 14 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Popular Question 15 months ago, created a question with more than 1,000 views. For merging VCF files
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: about collapsed and expanded vcf file
Scholar 17 months ago, created an answer that has been accepted. For A: about collapsed and expanded vcf file
Scholar 2.2 years ago, created an answer that has been accepted. For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
Scholar 2.2 years ago, created an answer that has been accepted. For A: BiocParallel example does not work any more (sbatch produced exit code 1)
Scholar 2.2 years ago, created an answer that has been accepted. For A: Genomic features for genomic positions

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