Moderator: russhh

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russhh5.1k
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Bioinformatics etc of leukaemia at University of Glasgow
 

Posts by russhh

<prev • 751 results • page 1 of 76 • next >
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Comment: C: Tripartite Network Construction
... Could you define what the contents of the three parts of the network should be, please? Is it 1) drugs, 2) genes with direct links to drugs, 3) genes that do not link to drugs but do link to members of 2. Is it just a visual representation of the tripartite-ness of the network that you want, or do y ...
written 3 hours ago by russhh5.1k
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Comment: C: conda/bioconda installation of plink fails
... Your install of numpy is probably pinned against MKL and blas, whereas plink is pinned against openblas (and having MKL/blas and openblas in the same env may cause some problems). There is a way to tell conda to use openblas whereever it wants blas: https://github.com/conda-forge/numpy-feedstock/iss ...
written 3 hours ago by russhh5.1k
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Comment: C: Gene symbol convert to Entrez ID
... But, to store the data, just use assignment: `gene_data <- AnnotationDbi::select(blah, blah, blah)` ...
written 8 days ago by russhh5.1k
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Comment: C: Gene symbol convert to Entrez ID
... It returns a data.frame. In R you have to be pretty explicit about which function you are using, and the code above might fail if you have `{dplyr}` (or another package that exports a `select` function / method) loaded. If the above doesn't work, you could try `AnnotationDbi::select()` to make it mo ...
written 8 days ago by russhh5.1k
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Comment: C: Struggling to work on a large Count Matrix
... Might be a job for {disk.frame} https://github.com/xiaodaigh/disk.frame ...
written 8 days ago by russhh5.1k
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Comment: C: Create a heatmap
... Yes you can do this. But if you have analysed the data using something like limma or edgeR, then your differential expression pipeline might already have computed the treatment means. You might be able to skip your averaging step and use precomputed results. ...
written 10 days ago by russhh5.1k
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Comment: C: Snakemake - generate an unkown file in input
... Then why not have a single output file name used by each run of your Rscript, and encode the mode-genotype within the file, rather than within the filename? ...
written 10 days ago by russhh5.1k
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Comment: C: Snakemake - generate an unkown file in input
... Could you explain in english what you want to do, please (rather than in approximate snakemake syntax). For each barcode, is there a single genotype associated with it? ...
written 10 days ago by russhh5.1k
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Answer: A: Snakemake - generate an unkown file in input
... Although this isn't a code review site, do you mind if I rewrite your workflow? I'll add some comments to cover any confusing bits that might be the source of your problem. I can't tell from your code whether `datapath` looks like "some/path/" or "some/path/some_prefix" (I've assumed the former), a ...
written 12 days ago by russhh5.1k
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Comment: C: Snakemake - generate an unkown file in input
... Sorry, how does your R-script know which of the genotypes are to be present in the output file? ...
written 12 days ago by russhh5.1k

Latest awards to russhh

Appreciated 10 weeks ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Mouse decoy assembly
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Popular Question 6 months ago, created a question with more than 1,000 views. For setting up MArrayLM objects for use in RUnit tests
Appreciated 7 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Appreciated 7 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 9 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
Appreciated 10 months ago, created a post with more than 5 votes. For C: Venn/Euler Diagram Of Four Or More Sets
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: fisher test with multiple samples
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: R survival analysis
Scholar 15 months ago, created an answer that has been accepted. For C: muTect analysis, error
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: R survival analysis
Popular Question 15 months ago, created a question with more than 1,000 views. For Has the RNA-Seq Atlas website closed?
Scholar 15 months ago, created an answer that has been accepted. For C: muTect analysis, error
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Unexpected outcome: Gene Enrichment using Fisher's Test
Scholar 16 months ago, created an answer that has been accepted. For C: muTect analysis, error

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