User: liz.ingsimmons

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Posts by liz.ingsimmons

<prev • 34 results • page 1 of 4 • next >
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Answer: A: Export annotation from GenomicInteractions package
... Hi there, You can use `as.data.frame` to turn the object into a data frame, and then select the columns you want to export, and export with e.g. `write.table`. ``` library("GenomicInteractions") library("GenomicRanges") data(hic_example_data) data(mm9_refseq_promoters) mm9_refseq_grl = split(mm9 ...
written 5 days ago by liz.ingsimmons140
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Excluding reads with a certain tag using tagFilter from Rsamtools
... Hi folks, I want to use `countBam` from `Rsamtools` to count the number of lines in a bam file matching certain criteria - mapping quality and *not* having the "XA" tag. On the command line, I would do this as follows: `samtools view -q 3 my_file_sort.bam | grep -v "XA:" | wc -l` However, I don' ...
rsamtools written 18 days ago by liz.ingsimmons140 • updated 18 days ago by Martin Morgan ♦♦ 23k
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Answer: A: Gviz (GenomicInteractions) arc height and boundaries
... Hi Nik, glad you are finding the GenomicInteractions package useful. The top of the arc doesn't appear to be cut off in your image, rather the arcs take up the full height of the panel. This is by design, and is similar to other Gviz track types where the y axis limits are set based on the values ...
written 5 weeks ago by liz.ingsimmons140
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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 5 months ago by liz.ingsimmons140
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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 5 months ago by liz.ingsimmons140
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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 5 months ago by liz.ingsimmons140 • updated 5 months ago by James W. MacDonald50k
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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 6 months ago by liz.ingsimmons140
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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 2.1 years ago by liz.ingsimmons140 • updated 2.1 years 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 3.2 years ago by liz.ingsimmons140
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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 3.2 years ago by liz.ingsimmons140

Latest awards to liz.ingsimmons

Popular Question 2.1 years ago, created a question with more than 1,000 views. For Error: Failed to set session genome to...
Popular Question 2.1 years ago, created a question with more than 1,000 views. For import wig to coverage
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Error: Failed to set session genome to...
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Error: Failed to set session genome to...
Scholar 3.2 years ago, created an answer that has been accepted. For A: Plotting genomic interactions in Gviz

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