User: H.Hasani

gravatar for H.Hasani
H.Hasani970
Reputation:
970
Status:
Trusted
Location:
Freiburg, Germany
Last seen:
5 days, 21 hours ago
Joined:
5 years, 2 months ago
Email:
h*************@yahoo.com

Posts by H.Hasani

<prev • 187 results • page 1 of 19 • next >
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Answer: A: How I produce such a plot in R
... In short yes, you can use [ggbeeswarm][1] to plot the individual observations along with with [ggsignif][2] to produce the statisics. However, if you are comparing the two groups that were measured by the same scale (MB) then you should plot them on the same scale, it will avoid misinterpreting the ...
written 5 months ago by H.Hasani970
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Answer: A: Statistical test for overlap
... I would use proportion test. As the name says, the null hypothesis is that the proportion in each set is the same. It helps you answer questions like do we have more male proportion in group A compared to female proportion in group B (test for two proportions); or if male proportion in the group is ...
written 7 months ago by H.Hasani970
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Comment: C: TCGAbiolinks problem downloading ASCAT2 data
... Just look into the help page of the function [GDCquery][1]! [1]: https://www.bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/query.html ...
written 7 months ago by H.Hasani970
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Answer: C: Survival analysis, K-M vs actuarial
... check this paper [Survival Analysis][1] [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5338193/ ...
written 7 months ago by H.Hasani970
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Answer: A: How do i reorder the bars in a grouped barplot
... you need to make `Concentration (ug/L)` as a factor, with levels ordered according to your need pest_ana[["Concentration (ug/L)"]] = factor (pest_ana[["Concentration (ug/L)"]] , levels =c("0% runoff", "20% runoff", "NOEC", "LC50")) hth ...
written 8 months ago by H.Hasani970
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Comment: C: Calculate correlations between ChipSeq data sets
... I would suggest [deeptools][1] [1]: https://deeptools.readthedocs.io/en/develop/ ...
written 10 months ago by H.Hasani970
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Comment: C: How to make a figure of gene mutation distribution like this using R language?
... Did you get it from a paper? if yes, you might find in their methods how they generated it, you can also contact the authors?! if you decide to use Lollipop, I would recommend [Lollipop-style mutation diagrams for annotating genetic variations][1] [1]: https://github.com/joiningdata/lollipops ...
written 10 months ago by H.Hasani970
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Answer: C: R: pedigree analysis
... I think it is because you have "0" as *dadid* and *momid*, you probably have to explicitly specify the parameter *missid* to "0" because *id* is not numeric or simply replace it by empty string. please check the [function's help page][1] [1]: https://www.rdocumentation.org/packages/kinship2/ve ...
written 10 months ago by H.Hasani970
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Comment: C: MultiQC not generating ouput ?
... yes, but according to output you are not. > [INFO ] multiqc : Searching : /home/doc/fastqgz/10_S9_R1_001.fastq.gz ...
written 11 months ago by H.Hasani970
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Answer: A: Create a heatmap
... why don't you annotate them using [ComplexHeatmap][1]? if you wanted to average over the stages then I wouldn't use heatmap for it, probably a boxplot with the different categories on one axis and the distribution of gene expression on the second axis. hth [1]: https://jokergoo.github.io/Complex ...
written 11 months ago by H.Hasani970

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Scholar 5 months ago, created an answer that has been accepted. For A: TCGA raw counts DexSeq
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