User: António Miguel de Jesus Domingues

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380
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Germany
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http://adomingues.gith...
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Posts by António Miguel de Jesus Domingues

<prev • 46 results • page 1 of 5 • next >
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Comment: C: DESeq2 design formula: single control for multiple conditions [RIP-seq]
... > You can see from re-arrangement of terms that your desired ratio is mathematically equal to RFK679 / Tyr101 *faceslap* Of course. way simpler than I thought. I probably missed those other posts because I was looking specifically at RIP-seq (and ChIP-seq) posts. It turns out I was over-thinkin ...
written 5 weeks ago by António Miguel de Jesus Domingues380
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Comment: C: DESeq2 design formula: single control for multiple conditions [RIP-seq]
... Hi Michael, Thank you for the quick reply. Maybe it was not very clear from my post (I rephrased it a little) but there are two parts to my analysis. The first, compare any condition vs N2, is kind of classic and I am following what you suggested, ~condition, followed by: results(dds, contrast=c("co ...
written 5 weeks ago by António Miguel de Jesus Domingues380
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DESeq2 design formula: single control for multiple conditions [RIP-seq]
... I am trying to calculate the enrichment of control (IgG) of an RIP-seq experiment. Since it was performed in triplicates, one approach I am exploring is using DESeq2 to take advantage of that replicate goodness. The goals: Determine enrichment of specific IPs over a background control. Possibly ...
deseq2 rip written 5 weeks ago by António Miguel de Jesus Domingues380
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Comment: C: Gviz: plotting multiple custom tracks or adding panel legend at the top
... Actually, I did find something strange about custom tracks:  when constructing them in a loop, it always takes the last element in the loop: ctracks <- list() for (i in 1:2){ print(i) ctracks[[i]] <- CustomTrack(plottingFunction = function(GdObject, prepare) {if(!prepare) grid.text( ...
written 12 months ago by António Miguel de Jesus Domingues380
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Gviz: plotting multiple custom tracks or adding panel legend at the top
... UPDATE: this issue was encountered in Gviz_1.14.7 and has been solved in (at least) Gviz_1.16.5. I am leaving it here in case someone using an older version comes across it.   I am trying to plot several data tracks (coverage), and to make it easier to identify the factors represented in each tra ...
gviz written 12 months ago by António Miguel de Jesus Domingues380 • updated 11 months ago by sergisayolspuig40
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Comment: C: biomaRt: Wormbase not working
... > Are you able to get information on transposons if you use the web interface at http://www.ensembl.org/biomart ? No. Only Searching directly in Wormbase. Regarding Wormbase and the issue with biomaRt not accessing it, I filled an issue in their github repo and got an answer. Relevant part is: ...
written 15 months ago by António Miguel de Jesus Domingues380
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Comment: C: biomaRt: Wormbase not working
... Well spotted Valery. It has been fixed now. ...
written 15 months ago by António Miguel de Jesus Domingues380
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biomaRt: Wormbase not working
... I have been trying to access WormBase using biomaRt in the hope of retrieving information for Transposon genes (eg WBTransposon00000001). I tried the instructions in the most recent vignette but it appears these are not correct:  library(biomaRt) wormbase=useMart("WS220",dataset="wormbase_gene") l ...
biomart wormbase written 15 months ago by António Miguel de Jesus Domingues380
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Comment: C: Plot ggplot2 and ggbio Images Together
... I didn't know either until I started poking around with str(). ...
written 2.4 years ago by António Miguel de Jesus Domingues380
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Comment: C: Plot ggplot2 and ggbio Images Together
... Could it be because the print call of ggbio is updating the plotting window? I have updated my answer with code that will plot 2 ggplots + 1 ggbio in 3 rows.   ...
written 2.4 years ago by António Miguel de Jesus Domingues380

Latest awards to António Miguel de Jesus Domingues

Popular Question 10 months ago, created a question with more than 1,000 views. For Gviz - show plus and minus strand from a bam
Popular Question 19 months ago, created a question with more than 1,000 views. For Extend GRanges start/end
Appreciated 19 months ago, created a post with more than 5 votes. For A: Plot ggplot2 and ggbio Images Together
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Plot ggplot2 and ggbio Images Together
Scholar 2.4 years ago, created an answer that has been accepted. For A: Plot ggplot2 and ggbio Images Together

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