User: H.Hasani

gravatar for H.Hasani
H.Hasani760
Reputation:
760
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Trusted
Location:
Freiburg, Germany
Last seen:
10 hours ago
Joined:
3 years, 8 months ago
Email:
h*************@yahoo.com

Posts by H.Hasani

<prev • 159 results • page 1 of 16 • next >
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Answer: A: How to calculate allele counts(Ref and alt) using a target bed file and aligned
... You can try GATK with `-L`, see [Intervals and interval lists][1] hth [1]: https://software.broadinstitute.org/gatk/documentation/article?id=11009 ...
written 18 days ago by H.Hasani760
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Comment: C: plotting problem with loop in R
... What does %*% do please? ...
written 4 weeks ago by H.Hasani760
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Comment: C: plotting problem with loop in R
... I see, then just use a second variable to get it running. The error is due to using the same variable to loop over the columns and rows leading to going beyond X's dimensions, i.e. by setting up the same value for both loops, X has only 18 columns yet n = 3173 = nrow(X). ...
written 4 weeks ago by H.Hasani760
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Comment: C: plotting problem with loop in R
... the error refers to this line v1 <- X[ , i] can you tell the outcome of the following: ncol(X) nrow(X) n by the way, in R you can easly use function *cor* on a full matrix instead of looping, see [Correlation matrix ...][1] [1]: http://www.sthda.com/english/wiki/correlati ...
written 4 weeks ago by H.Hasani760
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Comment: C: plotting problem with loop in R
... the function returns the plot, to have it save probably you need to pdf("myPlots.pdf") print(distance(args.....)) dev.off() ...
written 4 weeks ago by H.Hasani760
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Answer: A: Barplot with base point as 0.5
... I ran into this scenario before, what I did is the following: x*-1 for any X < my_cutoff then the trick in ggplot is to ggplot(df, aes(x=Genes,y=Ratio,fill=Group)) + .... + scale_y_continuous(breaks = seq(....), labels = abs(seq(...))) + coord_flip() so in short, negative values will ...
written 4 weeks ago by H.Hasani760
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Comment: C: plotting problem with loop in R
... what is exactly the problem? are you getting an error? no plot is generated? ...
written 4 weeks ago by H.Hasani760
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Comment: C: Recovering bam files after unknow deletion in the storage
... I would add my voice to Kevin Blighe; don't lose any more time and just go to a professional data recovery. ...
written 5 weeks ago by H.Hasani760
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Answer: A: Mutated gene based pathway enrichment
... You can try [geneontology][1] or [enrichr][2] if you are not an R user. You can also start with this thread [Tutorial: Easy way to do GO enrichment in R][3] and take it from there to explore other R packages. hth [1]: http://geneontology.org/ [2]: http://amp.pharm.mssm.edu/Enrichr/ [3]: ht ...
written 6 weeks ago by H.Hasani760
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Comment: C: How to run several one-way ANOVAs in R using on different categories?
... a small comment, you don't need to write `lmPerm::aovp` since you already loaded the library ...
written 6 weeks ago by H.Hasani760

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