User: reubenmcgregor88

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Posts by reubenmcgregor88

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Does "the biostars handbook" contain sections on DNA, RNA and AA sequence alignment with phylogenetic tree construction?
... I have some experience, through teaching myself, of using R for RNAseq, ChIPseq etc, but have started in a new field of research. Specifically I am working with bacteria and would like to, for example, be able to align specific regions of AminoAcids (which is used to split the bacteria I am studying ...
biostars handbook written 5 weeks ago by reubenmcgregor8840
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Comment: C: annotatePeaks.pl Homer using "RNA"
... Sorry I meant to ask about annotatePeaks.pl not the motif searching, I have updated the post ...
written 5 months ago by reubenmcgregor8840
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annotatePeaks.pl Homer using "RNA"
... Hi all, I have successfully used the following function in Homer to annotate my peaks to closest genes: annotatePeaks.pl    > i.e. annotatePeaks.pl ERpeaks.txt hg18   > outputfile.txt My problem is that some of my peaks are in the middle of introns of genes but are being called to ...
homer chip-seq motif written 5 months ago by reubenmcgregor8840 • updated 5 months ago by genomax42k
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Comment: C: ggplot2, point with border
... It is indeed (between ** below), which is why I am very confused at the random colour selection? vol + ggtitle(label = "Volcano Plot", subtitle = "Colored by fold-change direction") + geom_point(size = 2.5, alpha = 1, na.rm = T, shape=21, color = "black") + **scale_colour_m ...
written 6 months ago by reubenmcgregor8840
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Comment: C: ggplot2, point with border
... Thanks so much, This has made the following graph now, so colors and black surrounding working now: ![enter image description here][1] Sorry to be a pain, any idea why my color palette has been overwritten somehow? [1]: https://i.imgur.com/LgyfR7T.jpg > `vol <- ggplot(data, aes(x = lfc, ...
written 6 months ago by reubenmcgregor8840
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Comment: C: ggplot2, point with border
... Ah, gotcha. Thanks will remember this next time. ...
written 6 months ago by reubenmcgregor8840
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ggplot2, point with border
... Hi, Hoping someone can help with what may seem like a simple question. I would like to use ggplot2 to plot a graph with a black border but a custom fill. Using the following code I have managed to puoulate the graph as I would like it: # creating color palette >cols <- c("red" = "re ...
ggplot2 ggplot written 6 months ago by reubenmcgregor8840 • updated 6 months ago by e.rempel610
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Comment: A: Creating Interactive Volcano Plots with R and Plot.ly
... Great advice, just spent the morning honing my ggplot2 skills. Works nicely, thanks ...
written 6 months ago by reubenmcgregor8840
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Comment: C: Creating Interactive Volcano Plots with R and Plot.ly
... Hi Stephen, this is amazingly helpful and is really helping with getting my head around R language for plotting. I have a few ,what may be very simple questions. And feel free to point me towards other resources I should be reading. 1) How can I simply add a list of names that I specify from my g ...
written 6 months ago by reubenmcgregor8840

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