User: Charles Joly Beauparlant

Reputation:
160
Status:
Trusted
Location:
Canada
Website:
https://charlesjb.gith...
Twitter:
CharlesJolyB
Last seen:
5 months ago
Joined:
7 years, 4 months ago
Email:
c***********************@crchul.ulaval.ca

Posts by Charles Joly Beauparlant

<prev • 17 results • page 1 of 2 • next >
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Comment: C: DESeq2 significative fold change when both groups have no reads
... OK, I re-launched after changing the order of colData and it seems to correct the problem. Thank you for your input. Charles. ...
written 5 months ago by Charles Joly Beauparlant160
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DESeq2 significative fold change when both groups have no reads
... Hello, I’m observing an unexpected behavior from DESeq2. I obtain a significant padj when I compare the transcripts from 2 groups with 0 reads in all the replicates. > as.data.frame(res_F3POPS_vs_F3_CTRL) %>% rownames_to_column("id") %>% filter(id == "ENSRNOT00000088387") ...
deseq2 written 5 months ago by Charles Joly Beauparlant160 • updated 5 months ago by Michael Love20k
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Answer: A: metagene error when plot metagene reads signal
... Hello, The error happens when you have a region smaller than the bin_count parameter value. In your example, if genes is a GRanges object, you can test this by doing: summary(width(genes)) The min value should be smaller than 30. Depending on what you want to see with the metagene plot, you might c ...
written 11 months ago by Charles Joly Beauparlant160
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Comment: C: metagene ERROR in plot and other function
... Here is a new dropbox link: https://www.dropbox.com/s/ryg9xzcffh0m2vp/bin_explanation.pdf?dl=0 I added a Imgur link in case the dropbox one dies again: https://imgur.com/wo0UGio   ...
written 19 months ago by Charles Joly Beauparlant160
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Answer: A: Metagene: file import and aesthetic customization
... Hello JunLVI, Most function in the metagene object (except those starting with get_) silently returns the object itself to allow chaining. If you wish to extract the plot to customize it you can use the get_plot function after the plot() call. If you are familiar with ggplot2 and wish to have even ...
written 21 months ago by Charles Joly Beauparlant160
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Answer: A: metagene: paired-end bam as input
... Hello Anton, metagene does not support paired-end reads at the moment. If you use the design to group two paired bam files, it will treat them as replicates. Charles. ...
written 2.1 years ago by Charles Joly Beauparlant160
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Answer: A: metagene: moving the legend
... Hello Anton, The simplest way to tweak the visual representation of the metagene plot is to extract the plot with the get_plot function and use standard ggplot2 functions: mg$plot(title = "test metagene plot") p <- mg$get_plot() p + ggplot2::theme(legend.position="bottom") Cheers! Charles. ...
written 2.1 years ago by Charles Joly Beauparlant160
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Answer: A: metagene: strand orientation of plot?
... Hello Anton, By default, the strand orientation is not taken into account. But you do have the option to flip the regions based on the strand during the production of the matrices: mg <- metagene$new(regions = regions, bam_files = bam_files) mg$produce_matrices(flip_regions = TRUE) Cheers! ...
written 2.1 years ago by Charles Joly Beauparlant160
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Answer: A: metagene ERROR in plot and other function
... Hello arinaldi, The problem you have is because metagene will try to split all the regions into 100 bins by defaults to make sure all the regions have the same size. In your data, some regions are probably smaller than 100 nucleotides, which is why there is the error message you saw. You have two ...
written 2.4 years ago by Charles Joly Beauparlant160
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Comment: C: ENCODExplorer doesn't return results which are on the website
... I agree that it would make a lot of sense. And it should not be such a big change. But I have to prepare a test suite before adding it officially in the documentation/vignettes. I will also have to solve the ^ problem mentionned by Mike that is only applied to the first term. ...
written 2.7 years ago by Charles Joly Beauparlant160

Latest awards to Charles Joly Beauparlant

Scholar 19 months ago, created an answer that has been accepted. For A: metagene: strand orientation of plot?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: metagene: paired-end bam as input
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: metagene: strand orientation of plot?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: metagene: moving the legend
Scholar 2.6 years ago, created an answer that has been accepted. For A: metagene: paired-end bam as input
Scholar 2.6 years ago, created an answer that has been accepted. For A: metagene: strand orientation of plot?
Scholar 2.6 years ago, created an answer that has been accepted. For A: metagene: moving the legend

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