Bioconductor Changelog

Bioconductor Changelog

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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.	Thu, 10 Apr 2008 flowClust setMethods.R - put back default value in the replacement function namespace - quotation marks removed flowClust.c - comment out R_init_flowClust setMethods.R - remove default value in the replacement function all for testing only [/flowClust] permanent link MLInterfaces Added annotate to the Depends field. [/MLInterfaces] permanent link affycoretools Added AnnotationDbi to the Depends field. [/affycoretools] permanent link mdqc Moved cluster and MASS from Suggests field to the Depends. [/mdqc] permanent link Rintact Added RBGL and methods to the Depends field. [/Rintact] permanent link Ringo converted 'probeAnno' and 'ChIP-enriched region' into S4 classes, which also required some consecutive minor changes to other functions [/Ringo] permanent link sscore Update for compatibility with ExpressionSet class and minor bug fixes Update for compatibility with ExpressionSet class and minor bug fixes [/sscore] permanent link vsn Added lattice to the Depends field. [/vsn] permanent link affxparser more changes to the CHP parsing [/affxparser] permanent link yaqcaffy Moved geneplotter from Suggests to Depends field. [/yaqcaffy] permanent link plgem added a few argument checks to generate meaningful error messages in case argument 'covariateNumb' was not a number, or arguments 'q' or 'signLev' were outside the allowed range (i.e. between 0 and 1). [/plgem] permanent link Rtreemix Fixed man files to allow creation of Rtreemix-manual.pdf document. [/Rtreemix] permanent link Category bugfix, and bumped version update to include effect sizes in linear model test output [/Category] permanent link SNPchip the show method no longer returns the recycled vector of plotting symbols...this leads to problems when plotting multiple chromosomes [/SNPchip] permanent link xcms Add phenoData parameter to xcmsSet, and extract to a separate function the logic of deriving phenoData from a vector of paths. Rework API for extracting pipeline subsets (local vs ancestry) from xcmsData instances. Add check to profileMatrix<- to ensure histories of xcmsRaw and xcmsProfile are compatible. Moved Rgraphviz from Suggests to Depends field. [/xcms] permanent link VanillaICE Added Biobase to the Depends field. [/VanillaICE] permanent link biomaRt Updated getSequence example [/biomaRt] permanent link graph adding defaults to the nodeRenderInfo data [/graph] permanent link ppiStats Added AnnotationDbi and methods to Depends field. [/ppiStats] permanent link made4 Removing reference to soon-to-be defunct package arrayMagic from vignette. [/made4] permanent link Rgraphviz a number of fixes and additions to allow for various different node shapes. This is not functional yet... [/Rgraphviz] permanent link SLGI Added lattice and methods to the Depends field. [/SLGI] permanent link Biobase Removed reference of soon-to-be defunct package arrayMagic from vignette. [/Biobase] permanent link