search for: bioperl

Hi All, I have use the BLAST program provided by NCBI to compare large databases and have generated a lot of output in one long text file. I was looking for a way to parse out the results in a nice way so that it could be easily visualized. I was thinking of trying to write something in R, but I wanted to check in with the help group to make sure I am not re-inventing the wheel. Any help

I have a two part question one about statistical theory and the other about implementations in R. Thank you for all help in advance. (1) Am I correct in understanding that Heteroscedasticity is a problem for Generalized Additive Models as it is for standard linear models? I am asking particularly about the GAMs as implemented in the mgcv package. Based upon my online search it seems that some

I read some archived posts about calling R from Perl scripts. There seems to be an R package creating the necessaary interface. I'd like to do the opposite. That is to call Perl from an R script. I wonder whether this is possible at all ??? What about Bioperl which is a Perl variation built to deal with Bioinformatic datasets ? Thank you, Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

...96 4-Sep-2007 15:43 forUNIGENE 25447971 -rw-r--r-- 1 0 0 325655 1-Aug-2007 15:02 maize.out 25447972 -rw-r--r-- 1 0 0 264 1-Aug-2007 15:42 README 25447973 -rwxr--r-- 1 2522 2004 7209696 8-Aug-2007 14:53 bioperl-1.5.2_102.zip 25447974 drwxrwsr-x 9 2522 2004 4096 13-Aug-2007 14:59 bioperl-1.5.2_102 22610705 drwxr-xr-x 2 2522 2004 4096 14-Aug-2007 17:10 perl5lib 22610706 drwxr-xr-x 3 2522 2004 4096 14-Aug-2007 17:11 .cp...

...96 4-Sep-2007 15:43 forUNIGENE 25447971 -rw-r--r-- 1 0 0 325655 1-Aug-2007 15:02 maize.out 25447972 -rw-r--r-- 1 0 0 264 1-Aug-2007 15:42 README 25447973 -rwxr--r-- 1 2522 2004 7209696 8-Aug-2007 14:53 bioperl-1.5.2_102.zip 25447974 drwxrwsr-x 9 2522 2004 4096 13-Aug-2007 14:59 bioperl-1.5.2_102 22610705 drwxr-xr-x 2 2522 2004 4096 14-Aug-2007 17:10 perl5lib 22610706 drwxr-xr-x 3 2522 2004 4096 14-Aug-2007 17:11 .cp...

Hi all, I'm new to Centos, just moved here from Gentoo Linux. I have to install a server for bioinformatics purposes and I see that default yum repositories do not include any bioinformatics software (i.e. ncbi-toolkit, blat, and others). I'm googling a bit but I can't find a valuable solution: which is (or which are) the best repository I should add to have a satisfying list

On Wed, May 27, 2015 10:55 am, Zachary Giles wrote: > Mark, You might really want to compile torque from source (into an RPM > if you'd like) and redistribute that. Every version is a little wonky > and those of us that use(d) it often will poke around until we find a > version / patch-set that makes us happy and stick with that for a bit. > It's not an exact science and

...ioConductor [ not counting a handful of windows-only CRAN packages ] ), ESS editing in Emacs/XEmacs, GGobi visualization, Rpad webinterface, and initial support for the RKward GUI; - even stronger bioinformatics/biology support than before: BioConductor, arb, biofox, bioperl, biopython, blast2, boxshade, bugsx, clustalw, fastdnaml, fastlink, garlic, gromacs, hmmer, loki, mipe, molphy, muscle, ncbi, phylip, rasmol, readseq, seaview, t-coffee, textopo, and more; - continued strong mathematics / computational algrebra support: axiom,...

...ioConductor [ not counting a handful of windows-only CRAN packages ] ), ESS editing in Emacs/XEmacs, GGobi visualization, Rpad webinterface, and initial support for the RKward GUI; - even stronger bioinformatics/biology support than before: BioConductor, arb, biofox, bioperl, biopython, blast2, boxshade, bugsx, clustalw, fastdnaml, fastlink, garlic, gromacs, hmmer, loki, mipe, molphy, muscle, ncbi, phylip, rasmol, readseq, seaview, t-coffee, textopo, and more; - continued strong mathematics / computational algrebra support: axiom,...

...), ESS editing in Emacs / XEmacs, GGobi visualization, Rpad webinterface, the award winning JGR 'Java GUI for R', RSPerl, Rserve, an early release of the RKward GUI and more. - continued strong bioinformatics/biology support: BioConductor, arb, biofox, bioperl, biopython, blast2, boxshade, bugsx, clustalw, fastdnaml, fastlink, garlic, gromacs, hmmer, loki, mipe, molphy, muscle, ncbi, phylip, rasmol, readseq, seaview, t-coffee, textopo, ImageJ, and more; - continued strong mathematics / computational algrebra support: axiom,...

...), ESS editing in Emacs / XEmacs, GGobi visualization, Rpad webinterface, the award winning JGR 'Java GUI for R', RSPerl, Rserve, an early release of the RKward GUI and more. - continued strong bioinformatics/biology support: BioConductor, arb, biofox, bioperl, biopython, blast2, boxshade, bugsx, clustalw, fastdnaml, fastlink, garlic, gromacs, hmmer, loki, mipe, molphy, muscle, ncbi, phylip, rasmol, readseq, seaview, t-coffee, textopo, ImageJ, and more; - continued strong mathematics / computational algrebra support: axiom,...