Bioconductor Changelog

Bioconductor Changelog

	About Click here to learn more about this blog. Packages Click on a link for updates to that package only. ABarray ACME AffyCompatible AffyExpress AnnBuilder AnnotationDbi ArrayExpress BAC BCRANK BGmix BSgenome BioMVCClass Biobase BiocCaseStudies Biostrings BiostringsCinterfaceDemo BufferedMatrix BufferedMatrixMethods CALIB CGHbase CGHcall CGHregions CMA CORREP Category CoCiteStats DEDS DFP DNAcopy DynDoc EBImage EBarrays GEOmetadb GEOquery GGBase GGexplorer GGtools GLAD GOstats GSEABase GSEAlm GeneMeta GeneR GeneRfold GeneSelector GeneSpring GeneTraffic GeneticsBase GeneticsDesign GeneticsPed GenomeGraphs GlobalAncova GraphAT GraphAlignment HELP HEM Harshlight Heatplus HilbertCurveDisplay IRanges ITALICS Icens KEGGSOAP LBE LMGene LPE LPEadj MANOR MCRestimate MLInterfaces MVCClass MantelCorr MassSpecWavelet MeasurementError.cor MergeMaid Mfuzz MiPP OCplus OLIN OLINgui OrderedList OutlierD PCpheno PGSEA PROcess RBGL RBioinf RDocBook RLMM RMAGEML ROC RSNPper RWebServices RankProd Ratlpow RbcBook1 Rdbi RdbiPgSQL Rdisop RefPlus Resourcerer Rgraphviz Ringo Rintact RpsiXML Rredland Rrsat Rswub Rtreemix Ruuid SAGx SBMLR SIM SLGI SLqPCR SMAP SNPchip ScISI SemSim ShortRead TypeInfo VanillaICE XDE aCGH adSplit affxparser affy affyContam affyMvout affyPLM affyPara affyQCReport affycomp affycoretools affyio affylmGUI affypdnn altcdfenvs annaffy annotate annotationTools apComplex aroma.light arrayMagic arrayQuality arrayQualityMetrics beadarray beadarraySNP bgafun bgx bioDist biocGraph biocViews biomaRt bridge buildBioC cellHTS cellHTS2 cghMCR clusterStab codelink convert copa cosmo cosmoGUI ctc daMA diffGeneAnalysis domainsignatures dualKS ecolitk edd exonmap explorase externalVector factDesign fbat fdrame flowClust flowCore flowDB flowQ flowUtils flowViz gaga gaggle gcrma genArise geneRecommender genefilter geneplotter globaltest goCluster goProfiles goTools gpls graph hexbin hopach hypergraph idiogram impute iterativeBMA iterativeBMAsurv keggorth lapmix limma limmaGUI logicFS lumi maCorrPlot maDB maSigPro maanova macat made4 maigesPack makePlatformDesign makecdfenv marray matchprobes mdqc metaArray miRNApath minet multiscan multtest ncdfExts nem nnNorm nudge occugene oligo oligoClasses oneChannelGUI ontoTools pairseqsim pamr panp pathRender pcaMethods pcot2 pdInfoBuilder pdmclass pgUtils pickgene pkgDepTools plateCore plgem plier plw ppiStats prada preprocessCore prism puma quantsmooth qvalue rHVDM rama rbsurv reb rflowcyt rhdf5 rsbml rtracklayer safe sagenhaft seqLogo sigPathway siggenes simpleaffy simulatorAPMS sizepower smoothMiner snapCGH snpMatrix spikeLI spkTools splicegear splots spotSegmentation sscore ssize stam stepNorm tilingArray timecourse tkWidgets topGO twilight vbmp vsn weaver webbioc widgetInvoke widgetTools xcms xcmsGUI xps yaqcaffy Subscribe Subscribe to the Bioconductor Changlog.	Tue, 08 Apr 2008 GGtools introduce snps() for smlSet [/GGtools] permanent link rsbml Rework checking. All documents are checked after reading, so the 'check' argument is removed. It is replaced with 'quiet' which indicates whether the errors/warnings should be emitted. rsbml_check now has a 'verbose = FALSE' argument, which indicates whether libsbml 'info' and 'warning' messages are output to console (via message()). Libsbml errors now become R warnings and libsbml fatals now become R errors. Also fix some bugs in parsing libsbml3 constructs like the model history. Thought I had fixed these before, not sure what happened. [/rsbml] permanent link arrayQuality AP: added rd file for qcScore [/arrayQuality] permanent link GEOmetadb version bump for inclusion into Release 2.2 [/GEOmetadb] permanent link flowCore making sure that the samplesare in the same order after splitting. Also added a couple of updates to the documentation splitting using multipleFilterReuslts now lets you choose particular subpopulations [/flowCore] permanent link RBioinf This adds the package RBioinfo to the bioc repository [/RBioinf] permanent link genefilter editing genefilter continued, some minor man edits editing genefilter continued editing genefilter per discussion w/Robert, Florian [/genefilter] permanent link BAC Bumped the version number per Raphael's request. [/BAC] permanent link flowUtils Bumped the version numbers up to 0.99.0 to prepare for inclusion in BioC 2.2. [/flowUtils] permanent link flowQ Bumped the version numbers up to 0.99.0 to prepare for inclusion in BioC 2.2. [/flowQ] permanent link Category added a t() that was missing [/Category] permanent link XDE bumped version to signal release. Started adding methods for delta_gp model [/XDE] permanent link VanillaICE mostly updates to add needed documentation [/VanillaICE] permanent link rtracklayer Added rtracklayer to the bioc repository. [/rtracklayer] permanent link apComplex added plotComplex.R to render complex estimates [/apComplex] permanent link