Admin: Valerie Obenchain
Valerie Obenchain ♦♦ 6.5k
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Posts by Valerie Obenchain
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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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... 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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... 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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... 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
...
written 7 weeks ago by
Valerie Obenchain ♦♦ 6.5k
• updated 7 weeks ago by
funnyjokes1.com • 0
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... 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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... 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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... 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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... 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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... 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. ...
written 12 weeks ago by
Valerie Obenchain ♦♦ 6.5k
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... 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
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12 months ago,
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For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar
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For A: VariantAnnotation Installation Failure
Popular Question
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For Bioconductor 3.5 is released
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12 months ago,
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For A: AnnotationHub: confusing pValue/qValue for (some) Roadmap records
Scholar
12 months ago,
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For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
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For A: about collapsed and expanded vcf file
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For A: about collapsed and expanded vcf file
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For Bioconductor Package Archives
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For merging VCF files
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For Integer overflow when summing an 'integer' Rle
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For A: about collapsed and expanded vcf file
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For A: about collapsed and expanded vcf file
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14 months ago,
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For A: about collapsed and expanded vcf file
Teacher
14 months ago,
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For A: about collapsed and expanded vcf file
Teacher
15 months ago,
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For A: about collapsed and expanded vcf file
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15 months ago,
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For merging VCF files
Teacher
17 months ago,
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For A: about collapsed and expanded vcf file
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17 months ago,
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For A: about collapsed and expanded vcf file
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2.2 years ago,
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For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
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For A: BiocParallel example does not work any more (sbatch produced exit code 1)
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For A: Genomic features for genomic positions
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