User: Michael Lawrence

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Posts by Michael Lawrence

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Answer: A: IRanges:::coverage() speedup/enchancement
... On Mon, Nov 30, 2009 at 11:10 AM, Charles C. Berry wrote: > > > The semantics of the IRanges package and especially the RangedData class > are very apprpriate for some of the applications I deal with. > > Unfortunately, coverage() is too slow to be useful to me. > > I wonder ...
written 8.0 years ago by Michael Lawrence620
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Answer: A: import.gff3 bug in rtracklayer v1.6
... On Thu, Nov 26, 2009 at 12:35 AM, Hubert Rehrauer < Hubert.Rehrauer@fgcz.ethz.ch> wrote: > Dear all > > I used rtracklayer under R v 2.8.2 and everything worked fine. Now I > upgraded to R 2.10 and rtracklayer 1.6 > > When importing a gff3 file I get the following error: > ...
written 8.0 years ago by Michael Lawrence620
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Comment: C: Reg. rtracklayer and blocks
... On Wed, Nov 25, 2009 at 5:59 AM, Johannes Waage wrote: > Thank you for your reply. > > Trying to pass blockSizes as a column with i.e. "20,20", disrupts the > interaction with UCSC. My RangedData looks like this. > > RangedData with 24 rows and 9 value columns across 1 space > ...
written 8.0 years ago by Michael Lawrence620
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Answer: A: exon and transcription start site locations
... See the experimental data package called: GenomicFeatures.Hsapiens.UCSC.hg18. On Tue, Nov 24, 2009 at 2:39 PM, Paul Evans wrote: > Hi, > > I wanted to find out the exact locations on the genes (and the chromosome) > for exons and transcription start sites in the human genome. Is there ...
written 8.0 years ago by Michael Lawrence620
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Answer: A: Reg. rtracklayer and blocks
... On Mon, Nov 23, 2009 at 2:08 AM, Johannes Waage wrote: > Hi all, > > Rtracklayer interacts nicely with UCSC GB, but does anyone know if there is > support for uploading and displaying BED-tracks with thin and thick lines > (e.g. for visualizing splice-junction data from RNA-seq). > ...
written 8.0 years ago by Michael Lawrence620
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Answer: A: clustalW
... On Fri, Nov 20, 2009 at 12:52 AM, John Lande wrote: > dear all, > > is there a an implementation of clustalw in bioconductor? > > > No, but I've had success with running clustalw via system(), configuring it to use fasta for input and output. > -- > John > > ...
written 8.0 years ago by Michael Lawrence620
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Answer: A: Conservation tracks in BioC?
... On Fri, Nov 13, 2009 at 12:52 PM, Mercier Eloi wrote: > > Hi everyone, > > I get hundreds of TF binding sites and I would be interesting to acces > conservation data from UCSC. > I tried the ucscTableQuery but as mentionned Paul, there is no easy way to > send multiple queries. ...
written 8.0 years ago by Michael Lawrence620
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Answer: A: rtracklayer bed import
... On Fri, Oct 30, 2009 at 3:38 AM, Christian Ruckert wrote: > When trying to import the example .bed track from > http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED with the > import function from rtracklayer package I get the following error message: > > > tr = import("ex ...
written 8.1 years ago by Michael Lawrence620
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Answer: A: plotting multiple genes on a genome
... On Wed, Oct 21, 2009 at 4:32 AM, Jarek Bryk wrote: > Hello, > > I would like to plot a list of interesting genes (located on different > chromosomes) on a genome. I extracted their genomic coordinates with biomaRt > (see table below) and now I am looking for a way to send them all t ...
written 8.1 years ago by Michael Lawrence620
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Answer: A: Trans sites associated with a gene (Transfac database?)
... On Wed, Oct 7, 2009 at 12:08 PM, Tim Smith wrote: > Hi all, > > I wanted to get the trans factor sites that affect a set of genes. Is there > any package in bioconductor that will enable me to do this? > I don't know of any package that does this directly, but here are some tips. ...
written 8.1 years ago by Michael Lawrence620

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