User: rcavalca

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rcavalca130
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130
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United States
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rcavalcante
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2 weeks, 6 days ago
Joined:
3 years, 7 months ago
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r*******@umich.edu

Posts by rcavalca

<prev • 27 results • page 1 of 3 • next >
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Answer: A: annotatr: CpG Island/Shore/Shelf IDs
... Hi Stephany, Thanks for this suggestion. I think this is a good idea, but I'll need to spend some time thinking about how to do this because there are cases (I'm fairly sure) where islands may be close to each other and so they could potentially share a shore or shelf. Nevertheless, I'll put this ...
written 20 days ago by rcavalca130
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Comment: C: CpG site not annotated with annotatr
... Hi Sol, Since it is upstream, my guess would be that it would show up in the 1to5kb annotation. The promoter annotation only extends 1kb upstream from the TSS. I verified in the UCSC Genome Browser for hg19. As for the list of other CpGs, I looked at a handful at random and they seem to primarily ...
written 7 weeks ago by rcavalca130
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Answer: A: CpG site not annotated with annotatr
... Hi, Thanks for using annotatr. If it were 4kb upstream of a gene, I would answer that it falls in the 1to5kb regions, which is distinct from the promoters. However, you said 4kb downstream which suggests that it should probably be intergenic. To help me figure this out, could you give me the locati ...
written 8 weeks ago by rcavalca130
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Request to remove requirement for gr to have widths 1 in BSseq constructor
... Hi, I'm a big fan of bsseq because it is exactly the data structure I need for a package I maintain (methylSig) that tests for differential methylation (at CpGs and over regions). As of the Bioc 3.7 release it appears that a check in the BSseq constructor was added (I don't see a reference to it in ...
bsseq R package written 6 months ago by rcavalca130 • updated 6 months ago by emmascottgm0
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Comment: C: Strange error in bsseq when trying to assign seqinfo
... Sounds good, thanks for the fix! ...
written 7 months ago by rcavalca130
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Strange error in bsseq when trying to assign seqinfo
...   Hello, I'm having a strange issue in R 3.5.0 / Bioc 3.7 when trying to assign seqinfo to a bsseq object that I don't have in R 3.4.3 / Bioc 3.6. The particular error I get can be reproduced with the following code: # Do not load any libraries seqinfo_hg19 = GenomeInfoDb::Seqinfo(genome = 'hg19 ...
genomicranges bsseq genomeinfodb seqinfo written 7 months ago by rcavalca130 • updated 7 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: ENSEMBL database for annotatr
... Hello, Correct, annotatr uses the UCSC knownGenes database. If there was a TxDb package for hg19 that used ENSEMBL as its basis, it would be fairly easy to create the annotations, but I am not aware of such a TxDb package. As to your question about read_regions(), my understanding is that 1 is add ...
written 9 months ago by rcavalca130
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Answer: A: Unexpected results from annotatr
... Hello, The annotations in annotatr include all the transcripts for a particular gene. In this case Got1 has an annotation for knownGene transcript uc008hoj.1 as 1to5kb upstream of a TSS, and it overlaps an intron that transcript uc012bmb.1 has. And in this case, your input region intersects both of ...
written 9 months ago by rcavalca130
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Answer: A: 'fill_order' in annotatr
... Hello, "fill_order" to the ordering of the bars in the bar chart, and also the legend. annotatr doesn't do a prioritization, really. It reports all the intersections of a region with annotations. So if a region is in both a UTR and CDS, it will count towards each of those categories in the bar char ...
written 9 months ago by rcavalca130
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Answer: A: How can I use Annotatr on CDS?
... Hi, thanks for using annotatr. The CDS can be used with mm10_genes_cds. For a visual idea of where that falls: http://bioconductor.org/packages/release/bioc/vignettes/annotatr/inst/doc/annotatr-vignette.html#genic-annotations Hope that answers your question. ...
written 10 months ago by rcavalca130

Latest awards to rcavalca

Scholar 19 months ago, created an answer that has been accepted. For A: chipenrich mm10 error
Scholar 19 months ago, created an answer that has been accepted. For A: Chipenrich expected fit line
Scholar 19 months ago, created an answer that has been accepted. For A: 'fill_order' in annotatr
Scholar 19 months ago, created an answer that has been accepted. For A: Unexpected results from annotatr
Scholar 21 months ago, created an answer that has been accepted. For A: chipenrich mm10 error

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