Admin: Valerie Obenchain
Valerie Obenchain ♦♦ 6.2k
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Posts by Valerie Obenchain
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Answer:
A: SNPs in multiple locations
... Hi,
On the locateVariants man page it says this under the 'Value' section:
A ‘GRanges’ object with a row for each variant-transcript match.
This means a single SNP may be classified as more than one feature and each feature is returned as a separate row. For your example it sounds like the S ...
written 27 days ago by
Valerie Obenchain ♦♦ 6.2k
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... Hi,
I think results in rowRanges() and assays()$counts are consistent. The show method for RangedSummarizedExperiment displays the column names for assays()$counts instead of the row names and maybe that's the point of confusion. The contract for the class is that the rows of rowRanges() match the ...
written 4 weeks ago by
Valerie Obenchain ♦♦ 6.2k
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... The seqlevel() setter was modified last year to include a pruning.mode argument. The error message shows the code necessary to drop seqlevels in using this argument. This is documented, with examples, on the ?seqlevels man page.
If you are seeing this error from running a function in ggbio and not ...
written 4 weeks ago by
Valerie Obenchain ♦♦ 6.2k
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Answer:
A: No annotation for single SNPs
... Hi,
Yes, this is a bug.
* locateVariants(query, subject, region=AllVariants()) should return all 8 variant types described on the ?AllVariants man page
* 'upstream' and 'downstream' parameters in AllVariants() can be set for both PromoterVariants() and IntergenicVariants() but not IntronVariants( ...
written 5 weeks ago by
Valerie Obenchain ♦♦ 6.2k
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... I'm not an RStudio expert but yes, I would think restarting R within RStudio should delete the tmp/.
If you restarted R and still got the error it sounds like a problem on our end with the caching. I'll look into this further.
Valerie
...
written 8 weeks ago by
Valerie Obenchain ♦♦ 6.2k
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... Hi Andrew,
The issue you're seeing is related to a stale PACKAGES file. This file lists package versions - if it's stale then the version will not match that in the repository (e.g., trying to retrieve VariantAnnotation 1.22.0 when the package had moved on to 1.22.1 or greater).
There are a couple ...
written 8 weeks ago by
Valerie Obenchain ♦♦ 6.2k
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370
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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 3 months ago by
Valerie Obenchain ♦♦ 6.2k
8
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... 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 ...
written 3 months ago by
Valerie Obenchain ♦♦ 6.2k
• updated 12 weeks ago by
Hervé Pagès ♦♦ 12k
0
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175
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... Please tag your message with the package name, ChIPpeakAnno, so the author is aware of the question.
...
written 3 months ago by
Valerie Obenchain ♦♦ 6.2k
• updated 3 months ago by
Martin Morgan ♦♦ 20k
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2
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... 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 3 months ago by
Valerie Obenchain ♦♦ 6.2k
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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 A: about collapsed and expanded vcf file
Teacher
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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 A: about collapsed and expanded vcf file
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For A: about collapsed and expanded vcf file
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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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For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
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For A: Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowP
Appreciated
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For New Package Submission Process
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For A: AnnotationHub: two broad peaks from same url are not the same
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For A: inconsistent default of file suffix
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For A: GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
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For A: Genomic features for genomic positions
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For A: readGAlignmentPairs slow in problematic region
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For A: AnnotationHub: two broad peaks from same url are not the same
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For A: GenomicAlignments is too slow with summarizeOverlaps
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For A: Intersecting a Granges and a GRangesList using within
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For A: inconsistent default of file suffix
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