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 ArrayTools 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 HilbertVis HilbertVisGUI IRanges ITALICS Icens KEGGSOAP LBE LMGene LPE LPEadj MANOR MCRestimate MEDME MLInterfaces MVCClass MantelCorr MassSpecWavelet MeasurementError.cor MergeMaid Mfuzz MiPP OCplus OLIN OLINgui OrderedList OutlierD PCpheno PGSEA PLPE 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 arrayMvout arrayQuality arrayQualityMetrics beadarray beadarraySNP bgafun bgx bioDist biocGraph biocViews biomaRt bridge buildBioC cellHTS cellHTS2 cghMCR chipseq clusterStab codelink convert copa cosmo cosmoGUI ctc daMA diffGeneAnalysis domainsignatures dualKS ecolitk edd edgeR 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 logitT lumi maCorrPlot maDB maSigPro maanova macat made4 maigesPack makePlatformDesign makecdfenv marray matchprobes mdqc metaArray miRNApath microRNA minet multiscan multtest ncdfExts nem nnNorm nudge occugene oligo oligoClasses oneChannelGUI ontoTools pairseqsim pamr panp parody 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.	Fri, 28 Mar 2008 AnnotationDbi These changes add support for Plasmodium falciparum These changes add support to make databases and organism level packages for the malaria parasite Plasmodium falciparum. [/AnnotationDbi] permanent link affyPara Adds affyPara to bioconductor 2.2 [/affyPara] permanent link GSEABase updateObject for outdated serialized instances - 'annotation' generates an error advising that updateObject needs to be called - updateObject,GeneSetCollection calls updateObject on all objects, then re-initializes the GeneSetCollection mapIdentifiers,GeneColorSet,-methods exception test and tidy - new unit test - revised error message on failure - tidy of mapIdentifiers man page [/GSEABase] permanent link* flowCore fixed a number of bugs in data import and basic plotting functions [/flowCore] permanent link Rdisop Removing support for building on a Mac OS X until we can find a sub-make process that works. [/Rdisop] permanent link Ringo many minor improvements and clarifications [/Ringo] permanent link GEOquery Rebuilt Vignette [/GEOquery] permanent link prada Small change to vignette to get package to build. [/prada] permanent link xcms Fix NAMESPACE for new stages. Add prompt methods for stages and protocols. Remove filterProfile stage (and filterProfileBase protocol) and replace with more specific (and thus hopefully clearer in purpose) stages removeProfileBaseline and smoothProfile. Various other fixes. [/xcms] permanent link XDE corrected in diffExpressed_main.cpp that all arguments must be called by reference [/XDE] permanent link GlobalAncova small change in vignette [/GlobalAncova] permanent link