User: Malcolm.Cook

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Malcolm.Cook720
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720
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kansas, usa
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http://www.google.com/...
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19 hours ago
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7 years, 1 month ago
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Posts by Malcolm.Cook

<prev • 83 results • page 1 of 9 • next >
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Comment: C: Differential Expression of Splice Junctions using voom-limma/voom-diffSplice
... Hi Stefan, - re 0: thanks for your clarification on the adoption of DEXSeq - re 2-4: do I understand from this that you have 250 individual samples without any biological replicates? If so, this will challenge any differential analysis technique that relies upon variance analysis. However, y ...
written 4 days ago by Malcolm.Cook720
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Answer: A: Differential Expression of Splice Junctions using voom-limma/voom-diffSplice
... Please explain more carefully your experiment and the questions you want to put to your data. I ask because I expect you are really interested in the "expression of splice junctions" as compared to something else (say, roughly, "expression of exons". ) I guess this because you are considering DEXS ...
written 12 days ago by Malcolm.Cook720
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Comment: C: Cuffdiff promoter.diff is empty
... can you provide the content of contrasts.txt? ...
written 6 weeks ago by Malcolm.Cook720
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Comment: C: cuffdiff vs cuffnorm vs cuffquant
... Hi Devon, What in you view is contemporary update on cuffdiff's [Differential splicing tests][1] [1]: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#differential-splicing-tests---splicingdiff or does that still count as a "good reason" Thx! ...
written 9 weeks ago by Malcolm.Cook720
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Answer: A: problem in running vcf-consensus command
... You are correct that "...the reference file here refers to the reference DNA sequence including coding and non-coding parts of the genome." The answer to your question "Do I have to apply vcf-consensus to entire gene sequence first and then extract the relevant parts - which would be very tedious? ...
written 12 weeks ago by Malcolm.Cook720
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Answer: A: Create a UCSC chain file from a VCF
... I'm late to the QA party, but I hope a useful update for the contemporary searcher is the following list of options: * [vcf-consensus][1] (part of VCFtools)- "Apply VCF variants to a fasta file to create consensus sequence." * [FastaAlternateReferenceMaker][2] (part of Genome Analysis Toolkit - GA ...
written 3 months ago by Malcolm.Cook720
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Comment: C: The most popular Alternative to David?
... but, but, DAVID is up: https://david.ncifcrf.gov/ ...
written 3 months ago by Malcolm.Cook720
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Comment: C: How to sequentially replace a string with numerical value?
... Thanks for the education. And, I'm editing my old-school answer to adopt your use of `//=` instead of `||=`, which arguably is preferable. ...
written 4 months ago by Malcolm.Cook720
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Comment: C: How to sequentially replace a string with numerical value?
... Erhm, you caught me! I've not yet made the jump to Perl 6. Do you advise it? Most of what I used to do in Perl I now do in either bash, R, or python anyway... hmmm... ...
written 4 months ago by Malcolm.Cook720
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Comment: C: How to sequentially replace a string with numerical value?
... now that I've taken a look at what is [qqman][1], I like this approach better than any other, including mine, since qqman is an R pipeline, and this is an R solution. I'd go with something like: gwasResults$CHR=as.numeric(factor(gwasResults$CHR)) [1]: https://cran.r-project.org/web/package ...
written 4 months ago by Malcolm.Cook720

Latest awards to Malcolm.Cook

Scholar 5 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 15 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 2.4 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 2.9 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
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Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Which Are The Best Collections Of Bioinformatics Tools For Ngs Analysis And Sequ
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: How To Visualize Spliced Alignments Of Next Gen Sequencing Data?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table

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