Moderator: russhh

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russhh5.5k
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UK, U. Glasgow
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@haematobot
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Bioinformatics etc of leukaemia at University of Glasgow
 

Posts by russhh

<prev • 793 results • page 2 of 80 • next >
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Comment: C: Calculate enrichment factor from a list of GO terms
... Yes. You could try using `clusterProfiler::enricher` and pass in your GO-term to gene mappings with the `TERM2GENE` argument. This won't identify GO-term-depletions though. https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html ...
written 9 months ago by russhh5.5k
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Comment: C: How to avoid hardcoding in R? How to automatize R scripts?
... In addition to the answer by Yean, you might consider looking into the optparse and argparse packages. These make handling command line arguments easier. I have a template R-script that uses optparse here: [rscript-template gist][1] [1]: https://gist.github.com/russHyde/9d91fcb213973b0ace5424b05 ...
written 9 months ago by russhh5.5k
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Answer: A: Question about more complex makeContrasts from limma
... Let's suppose theres a gene that is 2-fold upregulated in phenotype1 relative to it's siblings and that is also 2-fold upregulated in phenotype2 relative to it's siblings (regardless of the lines). So this is a gene where the phenotype-induced change in expression is identical. log2(2) = 1, so we ...
written 10 months ago by russhh5.5k
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Comment: C: windows bioinformatics programs
... Although I agree with Dario, I've had more success running bioinformatics tools on the Windows subsystem for Linux, WSL, compared with cygwin: https://docs.microsoft.com/en-us/windows/wsl/install-win10 ...
written 10 months ago by russhh5.5k
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Comment: C: How to interpret different results in deseq2 due to different design
... Your second model assesses the effect of stage in a manner that is 'controlled' for the different baseline expression levels you'd get due to the different forms. ...
written 10 months ago by russhh5.5k
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Comment: C: Snakemake flow variantion
... You'd only include one of the functions in your actual Snakefile. Better to have a function than to stuff the same logic into a lambda IMO ...
written 10 months ago by russhh5.5k
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Comment: C: Snakemake flow variantion
... Are you sure you can do that (optional rule definition) on a sample-by-sample basis? ...
written 10 months ago by russhh5.5k
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Answer: A: Snakemake flow variantion
... The input to `C` can be a function that defines files based on the wildcard for the output from `C`. You could write a function that decides what the input to C should therefore be. When you say that "sometimes I would need X to take as input the output from B and then C to take the output from X", ...
written 10 months ago by russhh5.5k
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Comment: C: edger and continuous variables
... Thanks for posting your edgeR code. At no point did you ask why your results would be different using (the wildly inappropriate) edgeR::exactTest and (the completely appropriate) edgeR::glmQLFTest. exactTest is for testing for differences between groups and your glucose measurements do not define a ...
written 10 months ago by russhh5.5k
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Comment: C: edger and continuous variables
... (ATpoint made the comment) Just put the continuous variable in your design matrix. As you would in limma, or one of the linear regression models in R. And if the (extensive) documentation isn't sufficient for your needs, politely tell the author. You haven't provided any information about the model ...
written 10 months ago by russhh5.5k

Latest awards to russhh

Commentator 9 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 10 months ago, created an answer that has been accepted. For C: muTect analysis, error
Popular Question 10 months ago, created a question with more than 1,000 views. For setting up MArrayLM objects for use in RUnit tests
Scholar 10 months ago, created an answer that has been accepted. For C: muTect analysis, error
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 11 months ago, created an answer that has been accepted. For C: muTect analysis, error
Appreciated 15 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Popular Question 15 months ago, created a question with more than 1,000 views. For Mouse decoy assembly
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Popular Question 19 months ago, created a question with more than 1,000 views. For setting up MArrayLM objects for use in RUnit tests
Appreciated 19 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Appreciated 20 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 21 months ago, created an answer that has been accepted. For C: muTect analysis, error
Popular Question 22 months ago, created a question with more than 1,000 views. For setting up MArrayLM objects for use in RUnit tests
Appreciated 22 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: R survival analysis

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