User: Robert K. Bradley

Reputation:
40
Status:
New User
Location:
United States
Twitter:
@bradleybio
Last seen:
5 months ago
Joined:
4 years, 5 months ago
Email:
r*******@fredhutch.org

Posts by Robert K. Bradley

<prev • 22 results • page 1 of 3 • next >
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Answer: A: "quiet" mode for AnnotationHub?
... Thank you for the quick response. invisible doesn't seem to accomplish what I want, but suppressMessages does. Thanks for the simple fix suggestion. Best, Rob ...
written 10 months ago by Robert K. Bradley40
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"quiet" mode for AnnotationHub?
... Hello, I'm wondering whether there is a "quiet" mode for AnnotationHub, in which it would only print serious warnings or errors. Currently it displays snapshot and cache information whenever accessed. An example follows. I'm interested in such a "quiet" mode because I regularly access AnnotationHu ...
annotationhub written 10 months ago by Robert K. Bradley40
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Comment: C: error with downloading AnnotationHub item AH134
... Wonderful. Thank you! ...
written 12 months ago by Robert K. Bradley40
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Comment: C: error with downloading AnnotationHub item AH134
... Hi Valerie, Thank you for looking into this so quickly. I'd like to use the version 69 file if possible in order to ensure continuity with previous analyses that we've conducted using that version. (I know that the assembly should presumably be stable w.r.t. the version, but just to be sure I'll st ...
written 13 months ago by Robert K. Bradley40
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error with downloading AnnotationHub item AH134
... Hello, Downloading the AnnotationHub object AH134 (the hg19 genome) does not currently work, even though the source URL for that object exists and can be manually downloaded. Here is a reproducible code example: > library (AnnotationHub) Loading required package: BiocGenerics Loading required ...
annotationhub written 13 months ago by Robert K. Bradley40 • updated 13 months ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: GAlignments and the query sequence (SEQ) field of BAM files
... Thank you. This is perfect. On 10/21/15 11:39 AM, Hervé Pagès [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User Hervé Pagès <https: support.bioconductor.org="" u="" 1542=""/> wrote > Comment: G ...
written 2.1 years ago by Robert K. Bradley40
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Comment: A: GAlignments and the query sequence (SEQ) field of BAM files
... (To clarify, I am currently using narrow() on the DNAStringSet, which works fine; I'm just wondering if there is a more appropriate method that I should use to manipulate the metadata of a GAlignments object when the metadata is a string of length equal to the width of the read.) ...
written 2.1 years ago by Robert K. Bradley40
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Comment: A: GAlignments and the query sequence (SEQ) field of BAM files
... Hi Hervé, Thank you for the quick and very helpful response. I apologize for overlooking this feature of readGAlignments; it's exactly what I was looking for. I noticed that functions like qnarrow() don't affect the sequence when loaded as metadata (for understandable reasons). Is there a recommen ...
written 2.1 years ago by Robert K. Bradley40
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GAlignments and the query sequence (SEQ) field of BAM files
... Hello, I'm trying to figure out how to use Bioconductor for the following use case. I want to parse a subset of aligned reads from a BAM file, optionally trim the alignments, and then access the (possibly trimmed) query sequences. The first two operations--reading from the BAM file and trimming the ...
bam [galignments] written 2.1 years ago by Robert K. Bradley40
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Answer: A: threeUTRsByTranscript appears to not work after invoking setter seqlevelsStyle
... Hi Hervé, Thank you for looking into this. I'm looking forwards to the updated version of GenomicFeatures, and will let you know if I encounter any difficulties. Best, Rob ...
written 2.1 years ago by Robert K. Bradley40

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