Admin: Valerie Obenchain
Valerie Obenchain ♦♦ 6.2k
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Posts by Valerie Obenchain
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News:
Bioconductor 3.6 release
... The release of Bioconductor 3.6 will be Tuesday, October 31. Please see the schedule for details:
http://www.bioconductor.org/developers/release-schedule/
Over the next month we'll announce key deadlines on the bioc-devel mailing list:
https://stat.ethz.ch/pipermail/bioc-devel/
Part of pre ...
written 3 days ago by
Valerie Obenchain ♦♦ 6.2k
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... Please edit your question to show the error and the output of your sessionInfo().
...
written 10 days ago by
Valerie Obenchain ♦♦ 6.2k
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... I agree this can be confusing. The behavior of precede() and follow() were established years ago and are documented in both IRanges and GRanges on ?precede or ?follow. These definitions are from the GenomicRanges package, those in IRanges are very similar:
• precede: For each range in ‘x’, ...
written 15 days ago by
Valerie Obenchain ♦♦ 6.2k
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... The IntergenicVariants class has upstream and downstream values that define "how far" from the gene to search. Defaults are shown on the ?IntergenicVariants man page:
IntergenicVariants(upstream = 1e+06L, downstream = 1e+06L, idType=c("gene", "tx"))
If your SNP falls outside of these ranges it wo ...
written 15 days ago by
Valerie Obenchain ♦♦ 6.2k
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... Unfortunately I don't think there is a straightforward way of doing this. There is no metadata per se associated with the files.
Valerie
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written 22 days ago by
Valerie Obenchain ♦♦ 6.2k
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... I'm not sure why we see '**TTG**' for REFCODON - that's where the trouble starts. I can't try to reproduce this unless I know what annotation you used. Please edit your answer to include the annotation and the output of sessionInfo().
Valerie
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written 24 days ago by
Valerie Obenchain ♦♦ 6.2k
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... It's better to ask on one of the R / CRAN mailing lists:
https://www.r-project.org/mail.html
Valerie
...
written 4 weeks ago by
Valerie Obenchain ♦♦ 6.2k
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... Hi,
locateVariants() identifies hits in regions more specific than the at level of gene or transcript. Regions are documented on the ?AllVariants man page and are either parts of a gene or regions surrounding a gene.
CodingVariants()
IntronVariants()
FiveUTRVariants()
ThreeUTRVariants()
SpliceSit ...
written 5 weeks ago by
Valerie Obenchain ♦♦ 6.2k
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... The error says the tabix file doesn't have a chromosome named 'chr5'. Is this true? Have you checked the file to see how the chromosome names are represented? Depending on how the file was generated it might have just '5' with no 'chr' prefix or maybe there isn't any chromosome 5 data in there.
Val ...
written 7 weeks ago by
Valerie Obenchain ♦♦ 6.2k
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132
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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 12 weeks ago by
Valerie Obenchain ♦♦ 6.2k
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Scholar
3 months ago,
created an answer that has been accepted.
For A: about collapsed and expanded vcf file
Scholar
3 months ago,
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For A: about collapsed and expanded vcf file
Scholar
5 months ago,
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For A: about collapsed and expanded vcf file
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: about collapsed and expanded vcf file
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: about collapsed and expanded vcf file
Scholar
8 months ago,
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For A: about collapsed and expanded vcf file
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: about collapsed and expanded vcf file
Scholar
17 months ago,
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For A: distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
Scholar
17 months ago,
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For A: BiocParallel example does not work any more (sbatch produced exit code 1)
Scholar
17 months ago,
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For A: Genomic features for genomic positions
Scholar
17 months ago,
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For A: AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
Scholar
17 months ago,
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For A: Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowP
Appreciated
17 months ago,
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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
Scholar
17 months ago,
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For A: inconsistent default of file suffix
Scholar
17 months ago,
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For A: GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Teacher
17 months ago,
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For A: Genomic features for genomic positions
Teacher
17 months ago,
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For A: readGAlignmentPairs slow in problematic region
Teacher
17 months ago,
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For A: AnnotationHub: two broad peaks from same url are not the same
Teacher
17 months ago,
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For A: GenomicAlignments is too slow with summarizeOverlaps
Scholar
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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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18 months ago,
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For A: inconsistent default of file suffix
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