User: liz.ingsimmons

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Posts by liz.ingsimmons

<prev • 27 results • page 1 of 3 • next >
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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 17 months ago by liz.ingsimmons120 • updated 17 months ago by daniel.vantwisk30
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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 2.5 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 2.5 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 2.6 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 2.6 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 2.6 years ago by liz.ingsimmons120
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Comment: C: ENCODExplorer update snapshot: 404 error
... Oh, it works for me now on my laptop but not on our group's server. So I can just copy over the sqlite file. Maybe it's a problem with the server then.   ...
written 2.6 years ago by liz.ingsimmons120
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ENCODExplorer update snapshot: 404 error
... I'm trying to update my local snapshot of the ENCODE database to use with ENCODExplorer, however I get a 404 error. Any suggestions? tables = prepare_ENCODEdb(database_filename) [1] "Tue Mar 01 09:55:07 2016" Error in open.connection(con, "rb") : HTTP error 404. > traceback() 10: open.connectio ...
encodexplorer written 2.6 years ago by liz.ingsimmons120
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Comment: C: ENCODExplorer doesn't return results which are on the website
... Thanks, this does seem to be the problem. I wasn't expecting there to be such recent updates to the website, or for the snapshot to be more than six months old. ...
written 2.6 years ago by liz.ingsimmons120
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Error in ChIPQC: "Error in if (res >= minval) { : missing value where TRUE/FALSE needed"
... I would like to run ChIPQC on some ENCODE data downloaded using the ENCODExplorer package. Not all the samples have peaks available for download, however I'd still like to see e.g. % of reads in blacklist. I thought that this should be possible with ChIPQC, however I'm getting a (fairly uninformativ ...
chipqc written 2.6 years ago by liz.ingsimmons120 • updated 2.4 years ago by Rory Stark2.6k

Latest awards to liz.ingsimmons

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Error: Failed to set session genome to...
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Error: Failed to set session genome to...
Scholar 2.5 years ago, created an answer that has been accepted. For A: Plotting genomic interactions in Gviz

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