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.	Tue, 15 Apr 2008 AnnotationDbi Fixed bad but subtle bug in SQLforge. This fixes a bad bug in SQLforge that would under certain rare circumstances, map the wrong type of indentifier into the entrez gene field. Now the code does a better job of making sure that when it has an alternate ID, to find a correct entrez gene id if one can be found and stick that into the entrez gene field. [/AnnotationDbi] permanent link GGtools improvements to coalesce with encoDnaseI [/GGtools] permanent link oligoClasses added vignette for snp-level classes. updated man page for SnpLevelSet-class. [/oligoClasses] permanent link Ringo minor updates following up on introduction of S4 classes for probeAnno and ChIP-enriched regions and fixed a small bug in chromosomeNames method of probeAnno class [/Ringo] permanent link SAGx correction to unmatched brace in JT.test rd [/SAGx] permanent link RbcBook1 Removing dependence on defunct package arrayMagic. [/RbcBook1] permanent link quantsmooth Documentation to pass Check [/quantsmooth] permanent link affxparser Really updated to Fusion 1.10b. Fixed an error in the help page for readCel.R [/affxparser] permanent link Category bugfix to handle NA p-values [/Category] permanent link SNPchip synchronize HmmPredict and SnpLevelSet instances in plotSnp method. Add accessors/documentation. [/SNPchip] permanent link xcms Fixed : plotTIC won't work if object@tic slot is empty xcmsSet() now gives an error message if no data files were found docu updates & fixes More straightforward API for findPeaks.centWave, much less parameters are needed CAVE: peak width range (in seconds) is used instead of scale range CAVE: ppm instead of dev parameter [/xcms] permanent link GlobalAncova change in references change in vignette [/GlobalAncova] permanent link