User: Cassj

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Cassj1.3k
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Location:
London
Website:
http://mng.iop.kcl.ac.uk
Last seen:
6 years, 11 months ago
Joined:
8 years, 11 months ago
Email:
c****************@kcl.ac.uk

Bioinformatician in Noel Buckley's Molecular Neurobiology Group at the Institute of Psychiatry, King's College London. Mostly working with high throughput datasets relating to transcriptional regulation during neural cell differentiation.

I also run London BioGeeks

Posts by Cassj

<prev • 25 results • page 1 of 3 • next >
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Answer: A: Transcription Factor Enrichment
... Maybe RSAT? It seems to have a fairly broad collection of useful motif and CRM building and scanning tools, although I haven't used them myself yet so I can't tell you anything much about them. Web site/services are free but I think you have to register by post(?!) to install tools locally. http:// ...
written 8.3 years ago by Cassj1.3k
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Answer: A: Perl How To Isolate Fasta Sequences With A Range Of Values
... perl -ne '/length=(\d+)/; print if $1>=100' file.fa Seems to work. Neil's BioPerl method is far more reliable though ;) ...
written 8.4 years ago by Cassj1.3k
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Answer: A: Using Custom Cdfs In R
... Do you mean you don't want to use the existing Bioconductor packages, you want to build one from your own custom CDF file? If so, then maybe makecdfenv ...
written 8.4 years ago by Cassj1.3k
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Comment: C: Getting All Exons From Ensembl...
... If you've got the genome position and strand for each exon, could you maybe retrieve the sequences in Bioconductor, there seems to be D.rerio genome package - http://www.bioconductor.org/packages/release/Danio_rerio.html ...
written 8.5 years ago by Cassj1.3k
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Comment: C: Getting All Exons From Ensembl...
... which is exactly what Keith has already said while I was typing. Sorry! ...
written 8.5 years ago by Cassj1.3k
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Answer: A: Getting All Exons From Ensembl...
... What did you use as your biomart query? If you take the unique results from a query with no filters and attributes of Ensembl Gene ID, Ensembl Exon ID, Chr Start, Chr End and Chr Name then you get back 322622 exons. Results I got are here: http://mng.iop.kcl.ac.uk/~cassj/martquery_0804162753_537.txt ...
written 8.5 years ago by Cassj1.3k
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Answer: A: Reproducible Research: A More General Sweave?
... I'd be tempted to split your problem up a bit. 1. **Re-running of workflows** I tend to use Rake for this. Your assorted scripts and shell commands become a series of Rake tasks with appropriate dependencies defined in a Rakefile. There are lots of other tools for this, I'm sure people will r ...
written 8.6 years ago by Cassj1.3k • updated 5 months ago by RamRS20k
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Comment: C: Code Golf: Digesting Fasta Sequences Into A Set Of Smaller Sequences
... It's only re-inventing if it isn't better, or faster, or cooler, or shinier. If I've understood MTV correctly, I believe what you've done there is pimped the wheel ;) ...
written 8.6 years ago by Cassj1.3k
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Comment: C: Code Golf: Digesting Fasta Sequences Into A Set Of Smaller Sequences
... Just out of interest, what are you using the n-mers in the output file for? ...
written 8.6 years ago by Cassj1.3k
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Answer: A: Who Wants To Share Bookmarks Between Bioinformaticians
... http://delicious.com/cassj http://friendfeed.com/cassj ...
written 8.6 years ago by Cassj1.3k

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