User: David Lapointe

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Posts by David Lapointe

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Comment: C: [Rd] enabling reproducible research & R package management & install.package.ver
... There are utilities ( e.g. dotkit, and modules) which facilitate version management, basically creating on the fly PATH and env setups, if you are comfortable keeping all that around. David -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project. ...
written 6.2 years ago by David Lapointe170
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Answer: A: difference results by needle program and pairwiseAlignment
... I am not sure what your issue is. These sequences do not align well at all anyway. Global alignment is probably not a good way to compare them. There are large gaps at each end and 72% of the alignment ( according to needle) are gaps. Does pairwiseAlignment penalize end gaps? What score did pairwise ...
written 6.5 years ago by David Lapointe170
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Answer: A: Tktable 2.9 makefile problem
... Did you install the Tk and Tcl dev packages? -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Eric P Sent: Sunday, April 01, 2012 3:52 PM To: bioconductor at r-project.org Subject: [BioC] Tktable 2.9 makefile problem Hell ...
written 7.1 years ago by David Lapointe170
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Answer: A: OpenSuse 11.4, cannot install Bioconductor due to missing C compiler
... Well, it sounds like you don't have the compilers and/or devel packages loaded. Go into your package manager for openSUSE and make sure the compilers are checked ( C/Fortran) as well as the basic devel libraries. If not then install them. David -----Original Message----- From: bioconductor-bounces ...
written 7.4 years ago by David Lapointe170
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Comment: C: problem with using GSVA package
... I needed to install gsl-devel. Now it loads. Thanks -----Original Message----- From: Robert Castelo [mailto:robert.castelo@upf.edu] Sent: Monday, November 07, 2011 1:12 PM To: Lapointe, David Cc: bioconductor at r-project.org Subject: RE: [BioC] problem with using GSVA package hi, ok, it makes sen ...
written 7.6 years ago by David Lapointe170
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Comment: C: problem with using GSVA package
... Hi Robert, I am on Linux (Fedora 14) and gsl is installed as a RPM. I have updated to R 2.14. Other packages installed fine. David -----Original Message----- From: Robert Castelo [mailto:robert.castelo@upf.edu] Sent: Monday, November 07, 2011 12:24 PM To: Lapointe, David Cc: bioconductor at r-pro ...
written 7.6 years ago by David Lapointe170
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Comment: C: problem with using GSVA package
... This package looks interesting, but when I tried installing GSVA ( V1.20) it failed with "Cannot find the GNU Scientific Library >= 1.6" I have gsl-1.14 installed and the bioc web pages states gsl>=1.12 David -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioco ...
written 7.6 years ago by David Lapointe170
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Comment: C: problem with the KEGGSOAP package
... I wondered about this. At the bottom of the announcement link, Minoru adds: "Thank you for your immediate responses to this plea. I would like to emphasize that the KEGG web services, including the KEGG API, will be unaffected by the new mechanism to be introduced on July 1, 2011. Our policy for th ...
written 7.8 years ago by David Lapointe170
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Comment: C: Trans sites associated with a gene (Transfac database?)
... The free Transfac is very old. BioBase distributes current versions via subscription. Have you looked at Jaspar? http://jaspar.cgb.ki.se/. I use that with Emboss. David -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Beh ...
written 9.6 years ago by David Lapointe170
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Comment: C: Affymetrix annotation package
... I've noticed some discrepancies with annotations, also. At least for human, GeneCards has links from affy_id to other useful data. It is somewhat manual, though. Example: http://rcdev.umassmed.edu/cgi- bin/genecards/carddisp.pl?gene=POLE&search =1726_at&suff=txt -----Original Message--- ...
written 11.8 years ago by David Lapointe170

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