NIHR Biomedical Research Centre for Mental Health: Computational Biology
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Software

Matlab

We have a number of Matlab licenses installed on the cluster:

Shared software environment

In order to easily manage non-rpm packaged applications a NFS shared directory containing all applications is used, rather than using /usr/local/bin on each compute node. Using the base directory /share/, /share/apps – contains all applications installed in their own directory (eg. /share/apps/mega2_v4.5.0). Symbolic links are then used to point to the current version of the software (eg. /share/apps/mega2_current could point to /share/apps/mega2_v4.5.0. The directory /share/bin is then populated with symbolic links to all of the current applications listed in /share/apps. This is also true for /share/lib, /share/etc, /share/include. /share/bin is then PATHED by default.

A list of software that is installed is listed below:

[Last updated: October 23, 2011, 12:44 pm]

ApplicationVersionPathPathedWebsite
agile0.3.1/share/apps/agile_0.3.1Yes http://users.eecs.northwestern.edu/~smi539/agile.html
annovar20110117/share/apps/annovar_20110117Yes http://www.openbioinformatics.org/annovar/
ant1.8.1/share/apps/ant_1.8.1Yes http://ant.apache.org
atlas3.8.3/share/apps/atlas_3.8.3No http://math-atlas.sourceforge.net/
autoconf2.67/share/apps/autoconf_2.67No http://www.gnu.org/software/autoconf/
automake1.11/share/apps/automake_1.11No http://www.gnu.org/software/automake/
bam2pindel0.2.0/share/apps/bam2pindel_0.2.0Yes http://www.ebi.ac.uk/~kye/pindel/v_0.2.0
beagle3.2.1/share/apps/beagle_3.2.1Yes http://faculty.washington.edu/browning/beagle/beagle.html
beagle3.3.0b/share/apps/beagle_3.3.0bNo http://faculty.washington.edu/browning/beagle/beagle.html
BEDTools2.7.1/share/apps/BEDTools_2.7.1Yes http://code.google.com/p/bedtools/
BEDTools2.10.1/share/apps/BEDTools_2.10.1No http://code.google.com/p/bedtools/
blat34/share/apps/blat_34Yes http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
boost1.45.0/share/apps/boost_1.45.0No http://www.boost.org/
bowtie0.12.3/share/apps/bowtie_0.12.3No http://bowtie-bio.sourceforge.net/index.shtml
bowtie0.12.7/share/apps/bowtie_0.12.7Yes http://bowtie-bio.sourceforge.net/index.shtml
breakdancer1.1.20100719/share/apps/breakdancer_1.1.20100719Yes http://sourceforge.net/projects/breakdancer/
breakdancer1.1.20101025/share/apps/breakdancer_1.1.20101025No http://sourceforge.net/projects/breakdancer/
breakway0.7.1/share/apps/breakway_0.7.1Yes http://breakway.sourceforge.net/
bwa0.5.8a/share/apps/bwa_0.5.8aNo http://bio-bwa.sourceforge.net/
bwa0.5.8c/share/apps/bwa_0.5.8cNo http://bio-bwa.sourceforge.net/
bwa0.5.9/share/apps/bwa_0.5.9Yes http://bio-bwa.sourceforge.net/
CASAVAv1.8.0.tar.bz2/share/apps/CASAVA_v1.8.0.tar.bz2No Unavailable
CCRaVAT0.1/share/apps/CCRaVAT_0.1Yes http://www.sanger.ac.uk/resources/software/ccravat-qutie/
circos0.54.1/share/apps/circos_0.54.1Yes http://circos.ca/
CLUMP24/share/apps/CLUMP_24Yes http://www.smd.qmul.ac.uk/statgen/dcurtis/software.html
clustalw2.0.12/share/apps/clustalw_2.0.12Yes http://www.ebi.ac.uk/Tools/clustalw2/index.html
clusteralignv0.15/share/apps/clusteralign_v0.15No Unavailable
cnd1.2/share/apps/cnd_1.2Yes http://www.sanger.ac.uk/resources/software/cnd/
cnv-seq1.0/share/apps/cnv-seq_1.0Yes http://tiger.dbs.nus.edu.sg/CNV-seq/
consed20/share/apps/consed_20Yes http://www.phrap.org/
cufflinks0.9.1/share/apps/cufflinks_0.9.1No http://cufflinks.cbcb.umd.edu/
cufflinks0.9.3/share/apps/cufflinks_0.9.3No http://cufflinks.cbcb.umd.edu/
cufflinks1.0.1/share/apps/cufflinks_1.0.1Yes http://cufflinks.cbcb.umd.edu/
cytoscape2.6.3/share/apps/cytoscape_2.6.3Yes http://www.cytoscape.org
dmle2.3/share/apps/dmle_2.3Yes http://dmle.org/
dsrc0.3/share/apps/dsrc_0.3Yes http://sun.aei.polsl.pl/dsrc/
eigensoft3.0/share/apps/eigensoft_3.0Yes http://genepath.med.harvard.edu/~reich/Software.htm
EMBOSS6.3.1/share/apps/EMBOSS_6.3.1No http://emboss.sourceforge.net/
emmaxbeta07Mar2010/share/apps/emmax_beta07Mar2010Yes http://genetics.cs.ucla.edu/emmax/
epicenter1.7.0.8/share/apps/epicenter_1.7.0.8Yes http://www.niehs.nih.gov/research/resources/software/epicenter
exonerate2.2.0/share/apps/exonerate_2.2.0Yes Unavailable
fasta35.4.11/share/apps/fasta_35.4.11Yes http://www.ebi.ac.uk/Tools/fasta33/index.html
fastqc0.4.1/share/apps/fastqc_0.4.1No http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
fastqc0.9.0/share/apps/fastqc_0.9.0Yes http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
fastx-toolkit0.0.13/share/apps/fastx-toolkit_0.0.13Yes http://hannonlab.cshl.edu/fastx_toolkit/download.html
fluxcapacitor1.2-j1.5/share/apps/fluxcapacitor_1.2-j1.5Yes http://flux.sammeth.net/
freesurfer4.5.0/share/apps/freesurfer_4.5.0No http://surfer.nmr.mgh.harvard.edu/
freesurfer5.0.0/share/apps/freesurfer_5.0.0No Unavailable
freetds0.82/share/apps/freetds_0.82Yes http://www.freetds.org/
fsl4.1.6/share/apps/fsl_4.1.6Yes http://www.fmrib.ox.ac.uk/fsl/
gassst1.23/share/apps/gassst_1.23Yes http://www.irisa.fr/symbiose/projects/gassst/
gate5.2.1-build3581-ALL/share/apps/gate_5.2.1-build3581-ALLNo http://gate.ac.uk
gate6.0/share/apps/gate_6.0Yes http://gate.ac.uk/
gatk20100930/share/apps/gatk_20100930No http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit
gatk20110520/share/apps/gatk_20110520No http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit
gcp-gate6.0/share/apps/gcp-gate_6.0No http://gate.ac.uk/
gcp1.0/share/apps/gcp_1.0No http://gate.ac.uk/
gcp2.1/share/apps/gcp_2.1Yes Unavailable
gcp6.1/share/apps/gcp_6.1No http://gate.ac.uk/
gcpsvn/share/apps/gcp_svnNo Unavailable
gcta0.92.0-linux64/share/apps/gcta_0.92.0-linux64Yes http://gump.qimr.edu.au/gcta/index.html
GenomeAnalysisTK1.0.3471/share/apps/GenomeAnalysisTK_1.0.3471Yes http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit
GenomeAnalysisTK1.0.4905/share/apps/GenomeAnalysisTK_1.0.4905No http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit
git1.7.5/share/apps/git_1.7.5Yes http://git-scm.com
gmap20100727/share/apps/gmap_20100727Yes http://research-pub.gene.com/gmap/
GotoBLAS2/share/apps/GotoBLAS_2No http://www.tacc.utexas.edu/tacc-projects/gotoblas2/
granvil0.4/share/apps/granvil_0.4Yes http://www.well.ox.ac.uk/GRANVIL/
gsea22.06/share/apps/gsea2_2.06Yes http://www.broadinstitute.org/gsea/
gtool0.4.1/share/apps/gtool_0.4.1No http://www.stats.ox.ac.uk/~marchini/software/gwas/gtool.html
gtool0.6.6/share/apps/gtool_0.6.6Yes http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html
hapgen1.3.0/share/apps/hapgen_1.3.0Yes http://www.stats.ox.ac.uk/~marchini/software/gwas/hapgen.html
hapgen2.2.0/share/apps/hapgen_2.2.0Yes http://www.well.ox.ac.uk/~zhan/hapgen/hapgen2.html
haplopainter1.043/share/apps/haplopainter_1.043Yes http://haplopainter.sourceforge.net/index.html
haploview20110222/share/apps/haploview_20110222Yes http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/downloads#DOWNLOADS
hmmer3.0rc2/share/apps/hmmer_3.0rc2Yes http://hmmer.janelia.org/
/share/apps/igv.logNo Unavailable
IGVTools1.5.14/share/apps/IGVTools_1.5.14No Unavailable
igv1.5.34/share/apps/igv_1.5.34Yes http://www.broadinstitute.org/igv/
impute2.1.0/share/apps/impute_2.1.0No https://mathgen.stats.ox.ac.uk/impute/impute_v2.html
impute2.1.2/share/apps/impute_2.1.2Yes https://mathgen.stats.ox.ac.uk/impute/impute_v2.html
jags2.2.0/share/apps/jags_2.2.0Yes http://calvin.iarc.fr/~martyn/software/jags/
jpsgcs20100716/share/apps/jpsgcs_20100716No http://balance.med.utah.edu/wiki/index.php/JPSGCS
lamp0.0.9/share/apps/lamp_0.0.9Yes http://www.sph.umich.edu/csg/abecasis/LAMP/index.html
lapack3.1.1/share/apps/lapack_3.1.1No http://www.netlib.org/lapack/
libgtextutils0.6/share/apps/libgtextutils_0.6Yes http://hannonlab.cshl.edu/fastx_toolkit/download.html
locuszoom1.1/share/apps/locuszoom_1.1Yes http://csg.sph.umich.edu/locuszoom
locuszoom1.1.tgz.1/share/apps/locuszoom_1.1.tgz.1No Unavailable
mach1.0.16b/share/apps/mach_1.0.16bYes http://www.sph.umich.edu/csg/abecasis/MaCH/download
macs1.4.1/share/apps/macs_1.4.1Yes Unavailable
maq0.7.1/share/apps/maq_0.7.1Yes http://maq.sourceforge.net/
mathworksR2010A/share/apps/mathworks_R2010ANo http://www.mathworks.com/products/matlab/
mathworksR2010B/share/apps/mathworks_R2010BNo http://www.mathworks.com/products/matlab/
mecurial1.6/share/apps/mecurial_1.6Yes http://selenic.com/mercurial/
mega24.5.0/share/apps/mega2_4.5.0No http://watson.hgen.pitt.edu/docs/mega2_html/mega2.html
mega24.5.1/share/apps/mega2_4.5.1Yes http://watson.hgen.pitt.edu/docs/mega2_html/mega2.html
mendle10/share/apps/mendle_10Yes http://www.genetics.ucla.edu/software/download?package=1
mergedasm/share/apps/merged_asmNo Unavailable
merlin1.1.2/share/apps/merlin_1.1.2Yes http://www.sph.umich.edu/csg/abecasis/merlin/
metal201007/share/apps/metal_201007Yes http://www.sph.umich.edu/csg/abecasis/metal/
mgene0.1.0-beta/share/apps/mgene_0.1.0-betaYes http://www.fml.tuebingen.mpg.de/raetsch/suppl/mgene/
MISO20110715/share/apps/MISO_20110715No Unavailable
MISOcassj/share/apps/MISO_cassjYes Unavailable
/share/apps/mkdirNo Unavailable
mrbayes3.1.2/share/apps/mrbayes_3.1.2Yes http://mrbayes.csit.fsu.edu/
mrfast2.0.0.5/share/apps/mrfast_2.0.0.5Yes http://mrfast.sourceforge.net/
namd2.7b2/share/apps/namd_2.7b2Yes http://www.ks.uiuc.edu/Research/namd/
new_fugue2010-06-02/share/apps/new_fugue_2010-06-02Yes http://genome.sph.umich.edu/wiki/New_Fugue
novoalignCS1.01.04/share/apps/novoalignCS_1.01.04Yes http://www.novocraft.com/main/page.php?s=novoaligncs
novocraft2.07.05/share/apps/novocraft_2.07.05No http://www.novocraft.com/
novocraft2.07.09/share/apps/novocraft_2.07.09Yes http://www.novocraft.com/
p7zip9.13/share/apps/p7zip_9.13Yes http://p7zip.sourceforge.net/
palmapper0.4-rc3/share/apps/palmapper_0.4-rc3Yes http://www.fml.tuebingen.mpg.de/raetsch/suppl/palmapper
PeakSplitter1.0/share/apps/PeakSplitter_1.0Yes Unavailable
pedcheck1.00/share/apps/pedcheck_1.00Yes http://watson.hgen.pitt.edu/register/docs/pedcheck.html
pedscript2004/share/apps/pedscript_2004Yes http://genome.sph.umich.edu/wiki/PedScript#Download
penncnv2010May01/share/apps/penncnv_2010May01Yes http://www.openbioinformatics.org/penncnv/
phd2fasta0.990622.f/share/apps/phd2fasta_0.990622.fYes http://www.phrap.org/
phrap0.990329/share/apps/phrap_0.990329Yes http://www.phrap.org/
phred020425-c-acd/share/apps/phred_020425-c-acdNo http://www.phrap.org/
phred071220-b-acd/share/apps/phred_071220-b-acdYes http://www.phrap.org/
picard-tools1.26/share/apps/picard-tools_1.26Yes http://picard.sourceforge.net/
picard-tools1.35/share/apps/picard-tools_1.35No http://picard.sourceforge.net/
pindel20100806/share/apps/pindel_20100806Yes http://sourceforge.net/projects/pindel/
plinkseq0.05/share/apps/plinkseq_0.05No http://atgu.mgh.harvard.edu/plinkseq/index.shtml
plink1.07/share/apps/plink_1.07Yes http://pngu.mgh.harvard.edu/~purcell/plink/
plink1.08/share/apps/plink_1.08No ftp://gsapubftp-anonymous@ftp.broadinstitute.org
polya-svm2.2/share/apps/polya-svm_2.2Yes http://polya.umdnj.edu/PolyA_SVM/index.html
polyphred6.18/share/apps/polyphred_6.18Yes http://droog.gs.washington.edu/polyphred/
python2.5.2/share/apps/python_2.5.2No http://www.python.org/
python2.5.5/share/apps/python_2.5.5No http://www.python.org/
python2.7/share/apps/python_2.7No http://www.python.org/
qpalma0.9.2/share/apps/qpalma_0.9.2Yes http://www.fml.tuebingen.mpg.de/raetsch/suppl/qpalma
quantisnp1.1b/share/apps/quantisnp_1.1bNo http://www.well.ox.ac.uk/QuantiSNP/
quantisnp2.3/share/apps/quantisnp_2.3Yes http://groups.google.co.uk/group/quantisnp
rjungle1.0.361-mpi/share/apps/rjungle_1.0.361-mpiNo http://sourceforge.net/projects/randomjungle/
rjungle1.1/share/apps/rjungle_1.1Yes http://sourceforge.net/projects/randomjungle/
RSEQtools0.6/share/apps/RSEQtools_0.6Yes http://info.gersteinlab.org/RSEQtools/code
ruby1.9.2/share/apps/ruby_1.9.2Yes Unavailable
R2.8.1/share/apps/R_2.8.1No http://cran.r-project.org/
R2.10.0/share/apps/R_2.10.0No http://cran.r-project.org/
R2.12.0/share/apps/R_2.12.0Yes http://cran.r-project.org/
samstat20100915/share/apps/samstat_20100915Yes http://samstat.sourceforge.net
samtools0.1.9/share/apps/samtools_0.1.9No http://samtools.sourceforge.net/
samtools0.1.11/share/apps/samtools_0.1.11No http://samtools.sourceforge.net/
samtools0.1.15/share/apps/samtools_0.1.15No http://samtools.sourceforge.net/
savant1.2.1/share/apps/savant_1.2.1Yes http://compbio.cs.toronto.edu/savant/
scripture20101005/share/apps/scripture_20101005Yes http://www.broadinstitute.org/software/scripture/
SHRiMP1.3.1/share/apps/SHRiMP_1.3.1Yes http://compbio.cs.toronto.edu/shrimp
simwalk2.91/share/apps/simwalk_2.91No http://www.genetics.ucla.edu/software/simwalk_doc/
simwalk2.96-snp64/share/apps/simwalk_2.96-snp64Yes http://www.genetics.ucla.edu/software/simwalk_doc/
slope20101108/share/apps/slope_20101108Yes http://www-genepi.med.utah.edu/suppl/SLOPE/
snptest2.1.1/share/apps/snptest_2.1.1No http://www.stats.ox.ac.uk/~marchini/software/gwas/snptest.html
snptest2.2.0/share/apps/snptest_2.2.0Yes http://www.stats.ox.ac.uk/~marchini/software/gwas/snptest.html
soap2.20/share/apps/soap_2.20Yes http://soap.genomics.org.cn
sopra1.2/share/apps/sopra_1.2Yes http://www.physics.rutgers.edu/~anirvans/SOPRA/
splicemap3.3.5.2/share/apps/splicemap_3.3.5.2Yes http://www.stanford.edu/group/wonglab/SpliceMap
staden2.0.0b6-x86-64/share/apps/staden_2.0.0b6-x86-64Yes http://staden.sourceforge.net/
stampy1.0.11/share/apps/stampy_1.0.11Yes http://www.well.ox.ac.uk/project-stampy
svmerge1.0r19/share/apps/svmerge_1.0r19No Unavailable
SVMerge1.1r22/share/apps/SVMerge_1.1r22Yes http://svmerge.sourceforge.net
tabix0.2.5/share/apps/tabix_0.2.5Yes http://samtools.sourceforge.net/tabix.shtml Tabix
tesseract2.04/share/apps/tesseract_2.04Yes http://code.google.com/p/tesseract-ocr/
tophat1.1.0b/share/apps/tophat_1.1.0bNo http://tophat.cbcb.umd.edu/
tophat1.1.4/share/apps/tophat_1.1.4No http://tophat.cbcb.umd.edu/
tophat1.2.0/share/apps/tophat_1.2.0Yes http://tophat.cbcb.umd.edu/
trf4.04-linux64/share/apps/trf_4.04-linux64Yes http://tandem.bu.edu/trf/trf.html
ucsc-tools20110214/share/apps/ucsc-tools_20110214Yes http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
updatelinks1.00/share/apps/updatelinks_1.00Yes Unavailable
vancouvershortr4.0.15/share/apps/vancouvershortr_4.0.15Yes http://vancouvershortr.sourceforge.net/
variationhunter0.03/share/apps/variationhunter_0.03Yes Unavailable
vcftools0.1.3/share/apps/vcftools_0.1.3No http://vcftools.sourceforge.net/
vcftools0.1.5/share/apps/vcftools_0.1.5No http://vcftools.sourceforge.net
weka3.6.2/share/apps/weka_3.6.2Yes http://www.cs.waikato.ac.nz/ml/weka/

Shared CPAN environment

In order to minimise problems with managing multiple CPAN locations, dependencies and version, a shared CPAN library which is exported via NFS has been created. This is shared from the Panasas share: /share. CPAN is installed in the following location: /share/cpan

This greatly simplifies management and maintenance by having a single repository. It is relatively simple upgrade and rollback from failed updates, by simply backing up the repository before changes are made.

In addition to the modules specifically installed (and listed below) all dependent modules have also been installed.

Installed CPAN Modules

Bundle::CPAN
DBI
DBD::mysql 
MIME::Lite
File::Copy::Recursive
File::Tail
Compress::Raw::Zlib 
Sys::Syslog
Statistics::RankCorrelation
ExtUtils::F77
OpenGL
PDL
File::Cat
Net::SNMP
Crypt::DES
Crypt::Rijndael
Socket6
PerlIO::gzip
GD

Installed for BioPerl/Ensembl

Bundle::BioPerl
Bundle::Ensembl
Math::BigRat
bignum

Please contact for any additional modules to be installed.

Shared CRAN environment

To simplify the installation of R packages, a common repository for R packages has been created. This has been set up in /share/R/VERSION/library. This is shared out to all nodes in the cluster. By default the R_LIBS environment variable has been configured to include this path.

While there are a number of R versions installed, the current version of R which is maintained is 2.12.0. Below is a list of R modules which have been installed. For other versions of R, there will me modules installed in the appropriate path but are not listed below.

The Bioconductor base packages have been installed, along with following list of packages. Please contact for any additional packages to be installed.

List of installed CRAN modules

[Last updated: October 23, 2011, 12:44 pm]

abarray abind acepack acgh
ade4 ade4tkgui adegenet affxparser
affy affycomp affycoretools affydata
affyio affymetrixdatatestfiles affypdnn affyplm
affyqcreport akima allelic allmll
alr3 amelia ampaffyexample analyzefmri
annaffy annotate annotationdbi ape
aroma.affymetrix aroma.apd aroma.cn aroma.core
aroma.light arrayexpress arrayquality arrayqualitymetrics
ash aws bayesm beadarray
beadarraysnp beaddatapackr beta7 biobase
biodem biodist biomart biostrings
bit bitops boot bqtl
bsgenome bsgenome.ecoli.ncbi.20080805 bsgenome.hsapiens.ucsc.hg18 car
caret category catools cghbase
cghcall cghflasso cghmcr cghregions
chippeakanno chron class cluster
cma cmap cmprsk cntools
cnv cnvtools cocitestats coda
codetools colorspace combinat convert
corpcor cwhmisc databel date
dbi dclone degseq deldir
deseq design diagram digest
dnacopy doby domc dosnow
drc dynamictreecut dyndoc e1071
eco edd edger effects
ellipse epi epibasix epitools
estrogen exactranktests exonmap facsdorit
factdesign farma fasianoptions fassets
fastica fbasics fbonds fcalendar
fcopulae fecofin fexoticoptions fextremes
ff fgarch fields fimport
flashclust flexmix fmultivar fnonlinear
foptions foreach foreign fportfolio
fregression fseries ftrading funitroots
futilities g.data gam gap
gbm gcrma gdata gee
geepack genabel genefilter geneland
geneplotter genetics genomewidesnp5crlmm genomewidesnp6crlmm
genomicranges geoquery getopt ggbase
ggplot2 ggtools glad glasso
glmnet glmpath globaltest gmodels
go.db golubesets gosim gostats
gplots gpls graph gridbase
gseabase gstat gsubfn gtools
hapassoc haplo.ccs haplo.stats haplosim
hapmap100kxba hapmapsnp6 hdrcde hexbin
hgfocuscdf hgu133a2.db hgu133a2cdf hgu133acdf
hgu133atagcdf hgu133bcdf hgu133plus2cdf hgu2beta7
hgu95av2 hgu95av2.db hgu95av2cdf hgu95av2probe
hgug4112a.db hierfstat hilbertvis hmisc
hopach htqpcr hu6800.db hu6800cdf
hu6800probe human.db0 hwde hwriter
icens idiogram igraph illuminahumanv1.db
impute integrativeme ipred iranges
italics italicsdata iterators itertools
its kcsmart kegg.db keggsoap
kernlab kernsmooth kidpack kinship
ks lars latticeextra lddesign
ldheatmap leaps limma liquidassociation
lme4 lmgene lmtest locfit
lodplot logicreg logspline lpsolve
lumi lumibarnes lumihumanall.db lumihumanidmapping
lungexpression maanova magic makecdfenv
makeplatformdesign manor mapdata mapld
mapproj maps maptools maqcexpression4plex
marray masterbayes matchit matrix
matrixstats mboost mbpcr mclust
mcmcpack medips medme methylumi
mgcv misc3d mixomics mlbench
mlinterfaces mnormt mnp modeltools
mouse4302.db mouse4302cdf mouse4302probe msm
mstate multcomp multicore multtest
mvtnorm nlme nnet nws
oligo oligoclasses org.eck12.eg.db org.hs.eg.db
org.mm.eg.db org.sc.sgd.db ouch pamr
pcapp pd.hg18.60mer.expr pd.mapping250k.nsp pd.mapping250k.sty
pd.mapping50k.hind240 pd.mapping50k.xba240 pdinfobuilder pedigree
pegas pixmap plotrix plsgenomics
plyr polspline prada preprocesscore
princurve process prodata proto
pscl psy qpcrnorm qpgraph
qtl quadprog quantreg quantsmooth
qvalue r.cache r.css r.filesets
r.huge r.matlab r.methodss3 r.oo
r.rsp r.utils r2html r2winbugs
randomfields randomforest rbcbook1 rbgl
rcolorbrewer rcurl rda reb
relimp reshape rgl rglpk
rgtk2 ringo rjags rjsonio
rlecuyer rlmm rmetasim rmir
rmir.hs.mirna rmysql robustbase rocr
rpa rpart rpostgresql rrcov
rsamtools rsge rsqlite rsvgtipsdevice
rsymphony rtools4tb rtracklayer runit
samr sandwich scatterplot3d sciplot
scrime seqinr shape shortread
siggenes sim simpleaffy slam
sm smap sn snapcgh
snow snpassoc snpchip snplocs.hsapiens.dbsnp.20071016
snpmap snpmap.cdm snpmatrix sp
space spam sparsem spatial
spc spdep spikeinsubset ssoap
statmod strucchange subplex surveillance
survival svgannotation svmisc svmpath
tdthap tilingarray timedate timeseries
tkrplot topgo tree tripack
tseries urca vcd vgam
vsn waveslim wgcna xml
xmlschema xtable yeastcc yeastexpdata
zelig zoo