User: Malcolm.Cook

gravatar for Malcolm.Cook
Malcolm.Cook760
Reputation:
760
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Location:
kansas, usa
Website:
http://www.google.com/...
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Last seen:
1 week ago
Joined:
7 years, 6 months ago
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Posts by Malcolm.Cook

<prev • 93 results • page 1 of 10 • next >
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Comment: C: Future direction of Gene Set Enrichment Analysis
... Sidebar: I think GSEA should be reserved for this method: http://software.broadinstitute.org/gsea/index.jsp Do others agree? Disagree? ...
written 8 weeks ago by Malcolm.Cook760
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Comment: C: all samples in 0 cluster
... Just a guess, but many clustering programs I have seen reserve cluster 0 for all the elements that properly speaking are singletons... ...
written 8 weeks ago by Malcolm.Cook760
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Answer: A: Average intron length in Drosophila melagnoster
... A little R/BioConductor code will tell you the median is 102 and the mean is 1609: > library(TxDb.Dmelanogaster.UCSC.dm6.ensGene) > library(GenomicRanges) > i<-intronsByTranscript(TxDb.Dmelanogaster.UCSC.dm6.ensGene) > i<-unlist(i) > summary(width(i)) ...
written 8 weeks ago by Malcolm.Cook760
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Comment: C: Trying to modify new Repbase .embls to work as RepeatMasker .embl
... Hi, @muppetleague - wondering if you remember how you managed to get "Repbase .embls to work as RepeatMasker .embl"... Did you get it to support -species? Did you get it so work without -no_is ? Thanks! ...
written 3 months ago by Malcolm.Cook760
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Answer: A: Merge two bigwig(+/- strand) files from RNA-seq
... [WiggleTools](https://github.com/Ensembl/WiggleTools) which provides "Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency" should handle this swimmingly ...
written 4 months ago by Malcolm.Cook760
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Comment: C: MISO: Extraction of splicing events from user specified gene annotation (gtf or
... Since that is the documented method for creating MISO compatible annotation, you might consider your problem to be to the yarden's code to work. What did you try? What happened? ...
written 4 months ago by Malcolm.Cook760
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Comment: C: define alternative splice sites
... Actually I don't need the link, as I wrote, "I can not advise you on your use of dexseq for this purpose or interpretation of its output" ...
written 4 months ago by Malcolm.Cook760
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Comment: C: define alternative splice sites
... Hi - Sorry, I can not advise you on your use of dexseq for this purpose or interpretation of its output. (also, your link is to a non-existent page!). Cheers, Malcolm ...
written 4 months ago by Malcolm.Cook760
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Comment: C: Trying to use the gff_to_gtf utiilty in genomeTools
... For another approach to this conversion problem I recommend gffread http://ccb.jhu.edu/software/stringtie/gff.shtml ...
written 4 months ago by Malcolm.Cook760
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Answer: A: define alternative splice sites
... Hi NBS: If you provide * an exhaustive list of the varieties of "exon splicing events" you wish to define * descriptions of what you mean by each * an example or two of each given as a simulated junction.bed file ... then perhaps someone will be able or inclined to take your challenge. In m ...
written 4 months ago by Malcolm.Cook760

Latest awards to Malcolm.Cook

Scholar 10 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 20 months ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Scholar 2.8 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Scholar 3.3 years ago, created an answer that has been accepted. For A: Dataset's name in BioMart for S. pombe
Teacher 3.3 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 3.5 years ago, created an answer with at least 3 up-votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Demultiplex Illumina With Barcodes On Identifier Line
Teacher 3.5 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 3.5 years ago, created an answer with at least 3 up-votes. For A: How To Visualize Spliced Alignments Of Next Gen Sequencing Data?
Teacher 3.5 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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