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For plotting the inferred genetic networks GeneTS requires the "graph" and "Rgraphviz" packages (available from www.bioconductor.org). GMany functions for computing the NPMLE for censored and truncated data. !This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. pTwo-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation 8A package for processing protein mass spectrometry data. :demo of interface with full copy of all hpp defining boost CThis package can be used to handle MAGEML documents in Bioconductor $utilities for ROC, with uarray focus 4bindings to the XML RPC services of chip.org::SNPper Provides methods for accessing data stored in PostgreSQL tables. Code written by Timothy H. Keitt and modified by Jianhua Zhang jGeneric framework for database access in R. Code written by Timothy H. Keitt and modified by Jianhua Zhang This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package. vInterfaces R with the AT&T GraphViz library to provide the ability for plotting R graph objects from the graph package %A package to provide UUID values in R This package provides functions to puts SAGE library data into a datbase, calls genefinder to find genes that are similar to a given SAGE tag Tools for export and import Tree and Cluster to other programs This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. Statistical details are described in Bretz et al. (2003, submitted) Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids. Ctools for evaluating cohort distributions of gene expression levels ?Provides support for BerkeleyDB expression databases and views. Provides a subClass of exprSet from the Biobase package which implements the same features but uses an external matrix object with some arbitrary external storage. Basic class definitions and generics for external pointer based vector objects for R. A simple in-memory implementation is also provided. This package provides a set of tools for analyzing data from factorial designed micraorray experiments. 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GPL2.0 GPL GPL version 2 or newer GPL 2 LGPL LGPL GPL LGPL LGPL version LGPL GPL GPL GPL LGPL LGPL LGPL LGPL LGPL GPL version 2 or newer LGPL version 2 or newer GPL version 2 or newer GPL version 2 or newer GPL version 2 or newer LGPL GPL version 2 or newer LGPL LGPL BSD; read file BSD.license LGPL GPL version 2 or newer LGPL GPL GPL version 2 or newer GPL version 2 or newer LGPL BSD LGPL LGPL LGPL LGPL LGPL LGPL GPL version 2 or newer GPL2 LGPL LGPL LGPL GPL 2 GPL2.0 LGPL LGPL GPL version 2 or newer LGPL LGPL LGPL LGPL LGPL LGPL LGPL GPL2 GPL2 GPL version 2 or newer GPL2.0 GPL version 2 or newer LPGL LGPL GPL version 2 or newer LGPL LGPL free for non-commercial users. Non-academic users MUST have a valid license for the full (Excel) version of the SAM software programmed at Stanford University, see http://www-stat.stanford.edu/~tibs/SAM/index.html GPL version 2 or later LGPL LGPL LGPL GPL version 2 or newer LGPL AsIsR NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AsIsR NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AsIsR NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA Graphviz version 1.12 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA BerkeleyDB (>= 4.1) NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA HDF5 (1.4.x) NA NA NA NA NA Unix, Perl (>= 5.6.0), Netpbm NA AsIsR NA NA devel NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA devel NA NA devel NA NA AsIsR NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA AsIsR ./AnnBuilder_1.3.22.tar.gz OK  Tue May 4 06:31:43 2004 names File Status Rvers Date Source ./Biobase_1.4.10.tar.gz OK  Tue May 4 06:31:43 2004 File Status Rvers Date Source ./Biostrings_0.4.4.tar.gz OK  Tue May 4 06:31:43 2004 File Status Rvers Date Source ./DNAcopy_0.5-0.tar.gz OK  Tue May 4 06:31:43 2004 File Status Rvers Date Source ./DynDoc_1.3.14.tar.gz OK  Tue May 4 06:31:43 2004 File Status 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./RdbiPgSQL_1.0.6.tar.gz OK  Tue May 4 06:31:46 2004 File Status Rvers Date Source ./Rdbi_1.0.3.tar.gz OK  Tue May 4 06:31:46 2004 File Status Rvers Date Source ./Resourcerer_1.0.1.tar.gz OK  Tue May 4 06:31:46 2004 File Status Rvers Date Source ./Rgraphviz_1.3.28.tar.gz OK  Tue May 4 06:31:46 2004 File Status Rvers Date Source ./Ruuid_1.3.3.tar.gz OK  Tue May 4 06:31:47 2004 File Status Rvers Date Source ./SAGElyzer_1.3.2.tar.gz OK  Tue May 4 06:31:47 2004 File Status Rvers Date Source ./SNAData_1.1.0.tar.gz OK  Tue May 4 06:31:47 2004 File Status Rvers Date Source ./affyPLM_1.1.5.tar.gz OK  Tue May 4 06:31:47 2004 File Status Rvers Date Source ./affy_1.4.25.tar.gz OK  Tue May 4 06:31:48 2004 File Status Rvers Date Source ./affycomp_1.2.8.tar.gz OK  Tue May 4 06:31:56 2004 File Status Rvers Date Source ./affydata_1.3.1.tar.gz OK  Tue May 4 06:31:58 2004 File Status Rvers Date Source ./affylmGUI_0.4.5.tar.gz OK  Tue May 4 06:31:58 2004 File Status Rvers Date Source ./affypdnn_0.4-1.tar.gz OK  Tue May 4 06:31:59 2004 File Status Rvers Date Source ./altcdfenvs_0.1-5.tar.gz OK  Tue May 4 06:31:59 2004 File Status Rvers Date Source ./annaffy_1.0.7.tar.gz OK  Tue May 4 06:31:59 2004 File Status Rvers Date Source ./annotate_1.3.19.tar.gz OK  Tue May 4 06:31:59 2004 File Status Rvers Date Source ./arrayMagic_1.3.7.tar.gz OK  Tue May 4 06:32:02 2004 File Status Rvers Date Source ./arrayQuality_0.0.9.tar.gz OK  Tue May 4 06:32:02 2004 File Status Rvers Date Source ./bim_1.00-1.tar.gz OK  Tue May 4 06:32:03 2004 File Status Rvers Date Source ./convert_1.1.6.tar.gz OK  Tue May 4 06:32:03 2004 File Status Rvers Date Source ./ctc_1.2.7.tar.gz OK  Tue May 4 06:32:03 2004 File Status Rvers Date Source ./daMA_1.0.1.tar.gz OK  Tue May 4 06:32:03 2004 File Status Rvers Date Source ./ecolitk_0.2-8.tar.gz OK  Tue May 4 06:32:03 2004 File Status Rvers Date Source ./edd_1.2.6.tar.gz OK  Tue May 4 06:32:03 2004 File Status Rvers Date Source ./exprDB_0.1.4.tar.gz OK  Tue May 4 06:32:04 2004 File Status Rvers Date Source ./exprExternal_0.2.4.tar.gz OK  Tue May 4 06:32:04 2004 File Status Rvers Date Source ./externalVector_1.0.12.tar.gz OK  Tue May 4 06:32:04 2004 File Status Rvers Date Source ./factDesign_1.1.3.tar.gz OK  Tue May 4 06:32:04 2004 File Status Rvers Date Source ./gcrma_1.0.6.tar.gz OK  Tue May 4 06:32:04 2004 File Status Rvers Date Source ./genefilter_1.3.7.tar.gz OK  Tue May 4 06:32:04 2004 File Status Rvers Date Source ./geneplotter_1.3.14.tar.gz OK  Tue May 4 06:32:04 2004 File Status Rvers Date Source ./globaltest_2.1.4.tar.gz OK  Tue May 4 06:32:04 2004 File Status Rvers Date Source ./goTools_0.0.6.tar.gz OK  Tue May 4 06:32:05 2004 File Status Rvers Date Source ./gpls_1.0.4.tar.gz OK  Tue May 4 06:32:05 2004 File Status Rvers Date Source ./graph_1.2.16.tar.gz OK  Tue May 4 06:32:05 2004 File Status Rvers Date Source ./gtkWidgets_0.1.8.tar.gz OK  Tue May 4 06:32:05 2004 File Status Rvers Date Source ./hexbin_1.0.7.tar.gz OK  Tue May 4 06:32:05 2004 File Status Rvers Date Source ./impute_1.0.1.tar.gz OK  Tue May 4 06:32:05 2004 File Status Rvers Date Source ./limmaGUI_0.7.7.tar.gz OK  Tue May 4 06:32:06 2004 File Status Rvers Date Source ./limma_1.6.2.tar.gz OK  Tue May 4 06:32:06 2004 File Status Rvers Date Source ./makecdfenv_1.4.7.tar.gz OK  Tue May 4 06:32:07 2004 File Status Rvers Date Source ./marrayClasses_1.2.9.tar.gz OK  Tue May 4 06:32:07 2004 File Status Rvers Date Source ./marrayInput_1.1.9.tar.gz OK  Tue May 4 06:32:08 2004 File Status Rvers Date Source ./marrayNorm_1.1.11.tar.gz OK  Tue May 4 06:32:08 2004 File Status Rvers Date Source ./marrayPlots_1.1.13.tar.gz OK  Tue May 4 06:32:08 2004 File Status Rvers Date Source ./marrayTools_1.2.8.tar.gz OK  Tue May 4 06:32:09 2004 File Status Rvers Date Source ./marray_1.5.4.tar.gz OK  Tue May 4 06:32:09 2004 File Status Rvers Date Source ./matchprobes_1.0.6.tar.gz OK  Tue May 4 06:32:10 2004 File Status Rvers Date Source ./multtest_1.3.8.tar.gz OK  Tue May 4 06:32:10 2004 File Status Rvers Date Source ./ontoTools_1.2.5.tar.gz OK  Tue May 4 06:32:10 2004 File Status Rvers Date Source ./pairseqsim_0.2.tar.gz OK  Tue May 4 06:32:11 2004 File Status Rvers Date Source ./pamr_1.14.2.tar.gz OK  Tue May 4 06:32:11 2004 File Status Rvers Date Source ./pickgene_0.6.3.tar.gz OK  Tue May 4 06:32:11 2004 File Status Rvers Date Source ./prada_0.5.1.tar.gz OK  Tue May 4 06:32:11 2004 File Status Rvers Date Source ./qvalue_1.0.3.tar.gz OK  Tue May 4 06:32:11 2004 File Status Rvers Date Source ./rama_0.3.1.tar.gz OK  Tue May 4 06:32:11 2004 File Status Rvers Date Source ./reposTools_1.3.29.tar.gz OK  Tue May 4 06:32:11 2004 File Status Rvers Date Source ./rhdf5_1.3.4.tar.gz OK  Tue May 4 06:32:12 2004 File Status Rvers Date Source ./siggenes_1.0.6.tar.gz OK  Tue May 4 06:32:12 2004 File Status Rvers Date Source ./simpleaffy_1.09.tar.gz OK  Tue May 4 06:32:12 2004 File Status Rvers Date Source ./splicegear_1.0-5.tar.gz OK  Tue May 4 06:32:12 2004 File Status Rvers Date Source ./tkWidgets_1.5.6.tar.gz OK  Tue May 4 06:32:12 2004 File Status Rvers Date Source ./vsn_1.4.11.tar.gz OK  Tue May 4 06:32:12 2004 File Status Rvers Date Source ./webbioc_0.2.1.tar.gz OK  Tue May 4 06:32:12 2004 File Status Rvers Date Source ./widgetTools_1.2.8.tar.gz OK  Tue May 4 06:32:13 2004 File Status Rvers Date Source R Package Version Keywords Depends Title Suggests Uses Replaces Description URL Author Maintainer License Status Priority SystemRequirements ReleaseLevel Contains OSspecific KeySearchOrder row.namesR AnnBuilder:v:1.3.22 Biobase:v:1.4.10 Biostrings:v:0.4.4 DNAcopy:v:0.5-0 DynDoc:v:1.3.14 EBarrays:v:1.0-18 GOstats:v:0.7 GeneSpring:v:1.0.1 GeneTS:v:2.1.2 Icens:v:0.5 LPE:v:1.1.4 MeasurementError.cor:v:1.0.2 PROcess:v:0.9 RBGL:v:1.2.1 RMAGEML:v:2.0.6 ROC:v:1.0.9 RSNPper:v:1.0-0 RdbiPgSQL:v:1.0.6 Rdbi:v:1.0.3 Resourcerer:v:1.0.1 Rgraphviz:v:1.3.28 Ruuid:v:1.3.3 SAGElyzer:v:1.3.2 SNAData:v:1.1.0 affyPLM:v:1.1.5 affy:v:1.4.25 affycomp:v:1.2.8 affydata:v:1.3.1 affylmGUI:v:0.4.5 affypdnn:v:0.4-1 altcdfenvs:v:0.1-5 annaffy:v:1.0.7 annotate:v:1.3.19 arrayMagic:v:1.3.7 arrayQuality:v:0.0.9 bim:v:1.00-1 convert:v:1.1.6 ctc:v:1.2.7 daMA:v:1.0.1 ecolitk:v:0.2-8 edd:v:1.2.6 exprDB:v:0.1.4 exprExternal:v:0.2.4 externalVector:v:1.0.12 factDesign:v:1.1.3 gcrma:v:1.0.6 genefilter:v:1.3.7 geneplotter:v:1.3.14 globaltest:v:2.1.4 goTools:v:0.0.6 gpls:v:1.0.4 graph:v:1.2.16 gtkWidgets:v:0.1.8 hexbin:v:1.0.7 impute:v:1.0.1 limmaGUI:v:0.7.7 limma:v:1.6.2 makecdfenv:v:1.4.7 marrayClasses:v:1.2.9 marrayInput:v:1.1.9 marrayNorm:v:1.1.11 marrayPlots:v:1.1.13 marrayTools:v:1.2.8 marray:v:1.5.4 matchprobes:v:1.0.6 multtest:v:1.3.8 ontoTools:v:1.2.5 pairseqsim:v:0.2 pamr:v:1.14.2 pickgene:v:0.6.3 prada:v:0.5.1 qvalue:v:1.0.3 rama:v:0.3.1 reposTools:v:1.3.29 rhdf5:v:1.3.4 siggenes:v:1.0.6 simpleaffy:v:1.09 splicegear:v:1.0-5 tkWidgets:v:1.5.6 vsn:v:1.4.11 webbioc:v:0.2.1 widgetTools:v:1.2.8 data.frame Pkg df