User: JohnTownsend

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Posts by JohnTownsend

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Answer: A: Error in makeTxDbFromBiomart for fungi_mart
... I found the answer myself after a bit of digging around in the code for makeTxDbFromBiomart. The name of the mart for fungi has recently changed from fungal_mart to fungi_mart. However, this has not been reflected in the code for an internal function of the GenomicFeatures package: .get_EnsemblGen ...
written 3 hours ago by JohnTownsend0
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Error in makeTxDbFromBiomart for fungi_mart
... Hi, The function makeTxDbFromBiomart doesn't seem to be working when I try to access the fungi mart. I try myTxDb <- makeTxDbFromBiomart(biomart = "fungi_mart", dataset = "spombe_eg_gene", host="fungi.ensembl.org") and get the following error: Download and preprocess the 'transcripts' data ...
biomart genomicfeatures written 1 day ago by JohnTownsend0
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Cannot specify groups when overlaying aligned read tracks
... I am trying to overlay two sets of read depth data on a single track in Gviz. As a minimal example, I can get this data plotted on two tracks: library(Gviz) set.seed(1) coords <- seq(from=1000, to=5000, by=100) starts1 <- sample(1500:4500, 10) ends1 <- starts1 + 100 reads1 <- GRanges ...
gviz written 9 weeks ago by JohnTownsend0 • updated 9 weeks ago by Robert Ivanek430

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