User: izzy.yichao.cai

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Posts by izzy.yichao.cai

<prev • 6 results • page 1 of 1 • next >
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Arrange Gviz plotTracks() figure and basic R plot on a canvas
... Hi, I am trying to put Gviz output and a basic R plot on the same canvas. The figures I have: 1) A basic R plot recorded with recordPlot() 2) A bunch of Gviz tracks Attempts I took: I tried to grab the Gviz output using grid::grid.grabExp() and use cowplot::plot_grid() to put them on the sam ...
gviz gviz-package written 7 weeks ago by izzy.yichao.cai10
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Comment: C: Error selecting Gene Symbol using Entrez ID via Homo.sapiens
... What might be the cause of such genes that only appears only in org.Hs.eg.db but not in TxDb.Hsapiens.UCSC.hg19.knownGene? I have found a similar gene. GP1BB (entrez id: 2812) can not be found in TxDb.Hsapiens.UCSC.hg19.knownGene. It failed when I try to plot a gene track using Gviz package since n ...
written 9 months ago by izzy.yichao.cai10
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Comment: C: Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
... Thank you, James! Sorry for the incomplete output. I've noticed DDR1 has different transcripts on multi chromosomes. What I thought previously is that Gviz would collect all the transcripts in a specified region and collapse them into a single gene. However, it turns out that it would instead look ...
written 9 months ago by izzy.yichao.cai10
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Missing genes from TxDb.Hsapiens.UCSC.hg19.knownGene
... Hi all, I am trying to construct a gene track using TxDb. Hsapiens.UCSC.hg19.knownGene in Gviz package. I found a region that does not return any gene while when I look up in the TxDb there is actually transcripts.  Please see the following code that I used: library(Gviz) library(GenomicRanges) ...
gviz txdb txdb.hsapiens.ucsc.hg19.knowngene written 9 months ago by izzy.yichao.cai10 • updated 9 months ago by James W. MacDonald46k
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Gviz failed to fetch ideogram information from UCSC
... Hi all, I am trying to use Gviz to plot ideogram tracks. I was able to produce an ideogram in the past few weeks and it suddenly gets no reply from UCSC this week. The code I used: > IdeogramTrack(genome="hg19",chromosome="chr16",fontsize=30) Error in function (type, msg, asError = TRUE) : ...
gviz written 13 months ago by izzy.yichao.cai10
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Answer: A: r3Cseq problems in batch mode
... I have the same problem. Did you figure it out? ...
written 13 months ago by izzy.yichao.cai10

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