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.	Sat, 26 Apr 2008 GGtools added GGdata to suggests! [/GGtools] permanent link oligoClasses Fixing class nomenclature [/oligoClasses] permanent link gaga Updates by David Rossell to remove R CMD check WARNING messages. [/gaga] permanent link limma 25 April 2008: limma 2.13.10 - getEAWP() now gets probe names correctly from the rownames of object when object is a matrix. [/limma] permanent link flowCore paper: first paragraph for the outlook-application section [/flowCore] permanent link pdInfoBuilder Ensuring correct class for transcript_cluster_id field Gene ST arrays Ensuring correct class for crosshyb_type field Gene ST arrays changing readPgf/readClf to readPgfEnv/readClfEnv Fixing class nomenclature [/pdInfoBuilder] permanent link pamr Removed unused variable jj in fortran code. [/pamr] permanent link cellHTS2 I fixed the "clean" target in Makefile to delete large unwanted files after building the vignettes (this removes the size of the built package from 22MB to 5MB). [/cellHTS2] permanent link Biostrings Finished adding code to support the endGap argument to pairwiseAlignment. Added an endGap argument to pairwiseAlignment to allow users to ignore end gaps when performing pairwise alignments. [/Biostrings] permanent link GEOquery fixed for check [/GEOquery] permanent link BSgenome Following renaming of the BStringViews class -> XStringViews in Biostrings. Bumped version to 1.7.8. [/BSgenome] permanent link spkTools First commit spkTools package Adding spkTools, request by Rafa [/spkTools] permanent link XDE fixed bug in .integrativeCorrleationFilter [/XDE] permanent link oligo Fixing class nomenclature [/oligo] permanent link