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 GGtools GLAD GOstats GSEABase GSEAlm GeneMeta GeneR GeneRfold GeneSelector GeneSpring GeneTraffic GeneticsBase GeneticsDesign GeneticsPed GenomeGraphs GlobalAncova GraphAT GraphAlignment HELP HEM Harshlight Heatplus HilbertCurveDisplay 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 RLMM RMAGEML ROC RSNPper RWebServices RankProd Ratlpow RbcBook1 Rdbi RdbiPgSQL Rdisop RefPlus Resourcerer Rgraphviz Ringo Rintact RpsiXML Rredland Rtreemix Ruuid SAGx SBMLR SIM SLGI SLqPCR SMAP SNPchip ScISI SemSim ShortRead TypeInfo VanillaICE XDE aCGH adSplit affxparser affy 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 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, 24 Apr 2008 flowViz adding alias to man pages [/flowViz] permanent link rsbml Fix vignette for API changes. Update documentation for API changes in the rsbml_read and rsbml_check. commented out the sixth chunk in the vignette so at least it builds [/rsbml] permanent link pickgene Added description to man file to remove R CMD check warning. [/pickgene] permanent link Rdisop fix/add element definitions [/Rdisop] permanent link Biostrings Implemented the quality-based substitution matrix method of Ketil Malde. [/Biostrings] permanent link codelink 1.7.6 - added phenodata and feature data arguments to readCodelink2(). [/codelink] permanent link GeneticsDesign The power.casectl function was performing and invalid calculation. Replaced it with correct functions "GeneticsPower.Quantitative.Factor" and "GeneticsPower.Quantitative.Numeric", and modified the GeneticsBase Tutorial vignette to use the new functions. The old function is only present as a stub, which raises a depreciated error [/GeneticsDesign] permanent link flowQ added argument to control dimensions of the graphics importing missing function openHtmlPage in name space now [/flowQ] permanent link annotate wrapped the p2LL example in dontrun as the function is now deprecated [/annotate] permanent link explorase - Update filter column combobox when list name changes. - Make S expressions in filter dialog work. Remove BioC support for Mac OS X build of explorase. [/explorase] permanent link Category added doc pages to pass check [/Category] permanent link reb Fixed code/document inconsistency in man page. [/reb] permanent link GeneticsBase Correct description of power calculation example code Remove unrelated material from HOWTO The power.casectl function was performing and invalid calculation. Replaced it with correct functions "GeneticsPower.Quantitative.Factor" and "GeneticsPower.Quantitative.Numeric", and modified the GeneticsBase Tutorial vignette to use the new functions. The old function is only present as a stub, which raises a depreciated error [/GeneticsBase] permanent link