Moderator: Philipp Bayer

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Philipp Bayer6.3k
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PhilippBayer
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Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org

Posts by Philipp Bayer

<prev • 515 results • page 2 of 52 • next >
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Comment: C: How to get my tool on Homebrew ?
... Have a look at some other formulas - https://github.com/brewsci/homebrew-bio/blob/ea1b171f78eca1a8e2579d385ec6c80db9c09e2b/Formula/das_tool.rb has a few lines where it installs the ggplot2, doMC and data.table R-packages ...
written 16 days ago by Philipp Bayer6.3k
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Comment: C: How to get my tool on Homebrew ?
... `foo` is a placeholder for the software name, so if you wanted to create a new package called 'readAligner' you'd run brew create https://whatever_your_host_is/readAligner-v1.0.0.tar.gz # this will create something like /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/readAl ...
written 17 days ago by Philipp Bayer6.3k
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Answer: A: How to get my tool on Homebrew ?
... You will have to create a pull-request at the homebrew-bio repository with a new formula which details how your software is installed. You can read the guide here: https://github.com/brewsci/homebrew-bio/blob/master/CONTRIBUTING.md which links to this cookbook: https://docs.brew.sh/Formula-Cookbook. ...
written 17 days ago by Philipp Bayer6.3k
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Answer: A: Phylogenetic tree construction from small sized SNP data
... TASSEL can make simple cladograms from SNP data, that could work? https://www.maizegenetics.net/tassel ...
written 19 days ago by Philipp Bayer6.3k
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Comment: C: Need help to understand a problem in a R script
... Good idea, moved, thanks for that :) ...
written 25 days ago by Philipp Bayer6.3k
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Answer: C: Need help to understand a problem in a R script
... Could it be this: "UHR_Rep1","UHR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/UHR_Rep1" There's an extra space before '/media/' which maaaybe confuses ballgown ...
written 25 days ago by Philipp Bayer6.3k
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Comment: C: repeatmasker with my library
... This is correct, the output summary table checks for mostly human repeats - there is a script called `buildSummary.pl` in the util folder of RepeatMasker which builds a better summary based on the .out files See this for an output example https://www.biostars.org/p/170662/ ...
written 26 days ago by Philipp Bayer6.3k
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Comment: C: GO enrichment Analysis for Sus Scrofa using WGCNA in R
... Are you installing this on your own computer? lib = "anRichment"' is not writable means that you do not have write permissions on the folder where R tries to install the package. You can re-run R as administrator to maybe to get that working. ...
written 4 weeks ago by Philipp Bayer6.3k
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Answer: A: GO enrichment Analysis for Sus Scrofa using WGCNA in R
... First of all, WGCNA is deprecated and tells you to use a different package: NOTE: GOenrichmentAnalysis is deprecated. Please use function enrichmentAnalysis from R package anRichment, available from https://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/GeneAnnotation/ Second, WGCN ...
written 4 weeks ago by Philipp Bayer6.3k
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Answer: A: Change mean color in seaborn
... seaborn returns a matplotlib.axes object which you can manipulate just like any other matplotlib object, import matplotlib.pyplot as plt ax = sns.boxplot(x=your_data) # getp shows you all the properties of an axes object plt.getp(ax) You can then use plt.setp to manipulate al ...
written 5 weeks ago by Philipp Bayer6.3k

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