User: H.Hasani

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H.Hasani980
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Freiburg, Germany
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Posts by H.Hasani

<prev • 188 results • page 2 of 19 • next >
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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 13 months ago by H.Hasani980
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Answer: A: How extract gene TPM from GTEx?
... You need `GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt` instead of > GTEx_Analysis_v8_Annotations_SampleAttributesDD.xlsx the one you are using is meant to describe the columns of the actual "sampleAttributes" table ...
written 13 months ago by H.Hasani980
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Comment: C: ggplot second y-axis: how to specify a secondary axis if I don't want to scale m
... The `~.` means: use the values as defined in the `aes`, in your example it is `lkmean`. what comes after `~.` is a simple arithemtic operation. I'm not sure what exactly are you trying to reach by having two axises, but in principle, what you are doing is combining two plots merly because they shar ...
written 14 months ago by H.Hasani980
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Comment: C: ggplot second y-axis: how to specify a secondary axis if I don't want to scale m
... the function `scale_y_continuous` can be used without any scaling, like the ones in the example Ido has mentioned. If you look in the help of this function, you would know that the scaling happens when you specify the `trans` option ...
written 14 months ago by H.Hasani980
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TCGA mutations on Cbioportal
... Hello all, almost three years later I'm facing the same issue [here][1]. When using the downloaded data from Firehose, the number of mutations were more than the ones reported in cbioportal and particularly comparing with "provisional datasets", which according to cbioportal's FAQ it should contain ...
snp written 15 months ago by H.Hasani980
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Comment: C: grep with -f switch is not working
... well, that is the answer then! whatever you are grepping in that file doesn't match anything in the given directory due to spectial symbols and so! ...
written 15 months ago by H.Hasani980
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Comment: C: Removing a chromosome from a fasta file
... Is there a reason why this happens? dups sequences are understandable, but having one chromosome dups? are you working with cancer data? ...
written 15 months ago by H.Hasani980
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Comment: C: how can i find all of genes involve in special disease?
... check [DOSE][1] might be an option [1]: https://www.ncbi.nlm.nih.gov/pubmed/25677125 ...
written 15 months ago by H.Hasani980
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Comment: C: Annotate Affymetrix probesets to Gene symbols
... thank you very much, I'm still working on it, if I find something that might help others I'll post it. ...
written 16 months ago by H.Hasani980
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Comment: C: Annotate Affymetrix probesets to Gene symbols
... I'm getting no annotation, they simply disappear from the resulted table ...
written 16 months ago by H.Hasani980

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