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.	Thu, 21 Feb 2008 oligoClasses changed the chromosome and position methods for SnpLevelSet -- should work for combined objects added a method to combine instances of classes that extend SnpLevelSet [/oligoClasses] permanent link flowCore updated paper draft [/flowCore] permanent link cellHTS2 Tried to give some more explicit error messages in the function "checkColums", and now fill=FALSE in the read.table of the annotate method. [/cellHTS2] permanent link Biostrings More work on the PDict() constructor (now supports almost all kind of Trusted Band dictionaries, not only Trusted Prefix dictionaries, cropping the input sequences via the tb.start/tb.end/tb.width args is almost fully implemented). matchPDict() not yet ready to accept PDict objects with a head. Renamed the ULdna_PDict class -> CWdna_PDict. Version bumped to 2.7.24. More work on the PDict() constructor (changed its signature, the length of the Trusted Dictionary must now be specified via the 'tb.width' arg instead of the 'tb.end' arg). Version bumped to 2.7.23. [/Biostrings] permanent link tilingArray minor, cosmetic update to plotSegmentationHeatmap [/tilingArray] permanent link BufferedMatrixMethods (1.3.3) Change the documentation order of background correction and normalization. [/BufferedMatrixMethods] permanent link annotate Minor change in vignette text to reflect changes that were made to example code introduced in Revisions 16330, 23990, and 27757. [/annotate] permanent link affxparser Fixed the loading of R.utils in findFiles. This loading had bad consequences for R CMD check - unfortunately. A better fix would be to take care of the problem at its root. [/affxparser] permanent link oneChannelGUI Updated internal exon annotation. Refined filtering functions to be used for exon-level analysis. Added function for direct loading of affymetrix library files and location of apt tools directory [/oneChannelGUI] permanent link SNPchip moved chromosome and position methods to the oligoClasses package changed Depends to higher version of oligoClasses. UPdated vignette [/SNPchip] permanent link xcms Fixed gcc compiler Warning [/xcms] permanent link GOstats Minor change from exprSet to ExpressionSet in description and arguments section of this help file. [/GOstats] permanent link ppiStats i have started a file containing functions to generate summary statistics [/ppiStats] permanent link smoothMiner ylim in plot [/smoothMiner] permanent link