User: liz.ingsimmons

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Posts by liz.ingsimmons

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Comment: C: Unexpected behaviour of set operations on GRanges objects when dplyr is loaded
... Thank you very much for making this change! ...
written 3 months ago by liz.ingsimmons120
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Comment: C: Unexpected behaviour of set operations on GRanges objects when dplyr is loaded
... IMO this is a problem because the behaviour (`S4Vectors::union` being called) is unexpected, since at least in my experience this kind of behaviour doesn't happen in any other situations (either the correct method is called for the object, or an error occurs), because it produces significantly diffe ...
written 3 months ago by liz.ingsimmons120
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Unexpected behaviour of set operations on GRanges objects when dplyr is loaded
... Hi there, I'm getting unexpected behaviour when using set operation functions in an R session with both dplyr and GenomicRanges loaded. Set operation functions in dplyr used to not work on GRanges objects, which is fine, as if I accidentally used `union` rather than `GenomicRanges::union` I'd get a ...
genomicranges s4vectors dplyr written 3 months ago by liz.ingsimmons120 • updated 3 months ago by James W. MacDonald49k
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Answer: A: Visualizing 4c-seq as arc
... Hi there, Yes, you can use the GenomicInteractions package with 4C-seq data! It is designed to be suitable for any 3D genome interaction method. The makeGenomicInteractionsFromFile function gives some options for importing data, depending on the format of your input file. If your input is not in a ...
written 4 months ago by liz.ingsimmons120
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seqlevelsStyle for chrY in Drosophila?
... I'm trying to convert Drosophila seqinfo from UCSC to Ensembl style. However, using seqlevelsStyle to convert from UCSC to Ensembl style for dm6 does not give me what I expected - "chrY" is still "chrY" after the conversion whereas other chromosomes go from e.g. "chr2L" to "2L" (see below). Is this ...
genomeinfodb seqlevelsstyle dmel written 23 months ago by liz.ingsimmons120 • updated 23 months ago by daniel.vantwisk50
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Comment: C: Plotting genomic interactions in Gviz
... This functionality is also in the current release version, we just added the example in the vignette in the development version. I should also let you know we're switching over to using the new InteractionSet package as a backend in the next version of Bioconductor (released at the start of May), s ...
written 3.0 years ago by liz.ingsimmons120
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Answer: A: Plotting genomic interactions in Gviz
... Hi Enrico, The GenomicInteractions package includes a function to create an 'InteractionTrack' object for plotting with Gviz. You can see an example at the end of the vignette here. There are some further examples in the paper, and R scripts to generate those figures are provided as additional file ...
written 3.0 years ago by liz.ingsimmons120
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Comment: C: manipulate bedpe format files
... GenomicInteractions can export to igraph format, maybe the igraph package has some functions which would be useful for you. ...
written 3.1 years ago by liz.ingsimmons120
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Comment: C: ENCODExplorer doesn't return results which are on the website
... Oh, that is interesting that it doesn't actually support the Boolean operators - using `|` works quite well considering that! I'd strongly support adding official support for this - it's useful to be able to search for multiple cell lines and targets at once, and the alternative is nested for loops ...
written 3.1 years ago by liz.ingsimmons120
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Comment: C: ENCODExplorer doesn't return results which are on the website
... Sorry to un-accept your answer, but I've found that the example I gave was misleading. The final bed file on that page can't be found by queryEncode in some situations -- but does exist in the up-to-date encode_df I've managed to create. I think the problem may be that some bed files have NA values ...
written 3.1 years ago by liz.ingsimmons120

Latest awards to liz.ingsimmons

Popular Question 23 months ago, created a question with more than 1,000 views. For Error: Failed to set session genome to...
Popular Question 23 months ago, created a question with more than 1,000 views. For import wig to coverage
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Error: Failed to set session genome to...
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Error: Failed to set session genome to...
Scholar 3.0 years ago, created an answer that has been accepted. For A: Plotting genomic interactions in Gviz

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