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 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 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 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 ecolitk edd exonmap explorase externalVector factDesign fbat fdrame flowClust flowCore flowQ flowUtils flowViz gaga gaggle gcrma genArise geneRecommender genefilter geneplotter globaltest goCluster goProfiles goTools gpls graph hexbin hopach hypergraph idiogram impute keggorth lapmix limma limmaGUI logicFS lumi maCorrPlot maDB maSigPro maanova macat made4 maigesPack makePlatformDesign makecdfenv marray matchprobes mdqc metaArray 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 Jan 2008 AnnotationDbi Adds support to make most chip and organism sqlite files This update adds many new functions to add functionality to make many new kinds of organism and chip based sqlite files. In general there is a master function for each schema that adds the ability to make sqlite files of that type (with correct parameters). These functions will later be wrapped in another function that should call these functions and then also call makeAnnDbPkg() to make the sqlite file and then wrap it up in a new package. [/AnnotationDbi] permanent link bioDist increased version documented list method (and maybe wrote it too) [/bioDist] permanent link pdInfoBuilder Added extra annotation for CNV probes on SNP 5/6 arrays [/pdInfoBuilder] permanent link Biostrings Added "matchLRPatterns" and "matchProbePair" methods for BStringViews objects. No version bump. Made the "show" methods for BString, BStringViews and BStringAlign objects "getOption('width') aware" so that the user can control the width of the output they produce. No version bump. [/Biostrings] permanent link oneChannelGUI Adding Alternative splicing visualization for one gene-level probeset Adding conversion, for exon arrays, from gene-level probe set to genebank accession number Extending to exon arrays, limma topTable, the possibility to create template A for Ingenuity Knowledge Base Adding a filter to subset alternative splicing events using MiDAS p-values/RP p-values/average mean SI difference [/oneChannelGUI] permanent link xcms fixes for and in xcmsMSn vignette and documentation added missing xcmsProtoFilterProfile Merged manpages, removed illegal filename added METLIN XML reader URL:metlin.scripps.edu/download/MS.XML\nAdded basic ppm and ppmDev\nAdded array matching [/xcms] permanent link arrayQualityMetrics Change score table and experiments/arrays [/arrayQualityMetrics] permanent link