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, 15 May 2008 AnnotationDbi Fixes bug in inparanoid mappings. This was a bad bug that prevented these mappings from filtering out all the non-seed regions properly. [/AnnotationDbi] permanent link oligoClasses Updated classes definitions and initialization methods [/oligoClasses] permanent link GEOmetadb Helped fix a bug in geoConvert. Closed a database connection that was left open. [/GEOmetadb] permanent link flowCore minor fixes: typo and biblio [/flowCore] permanent link ShortRead make countLines arguments consistent with list.files, etc make countLines arguments consistent with list.files, etc [/ShortRead] permanent link SIM Adds package SIM to the bioc repository. [/SIM] permanent link Biostrings added the read.gapMask() function for extracting a mask from a UCSC "gap" file Converted the profiles slots in XStringAlign from numeric to XNumeric. Refactored pairwiseAlignment to optimize on scoreOnly setting. Optimized memory usage for pairwiseAlignment when scoreOnly = TRUE. Modified the pairwiseAlignment algorithm to use less memory. It is a little slower now, but can align short reads against much larger strings. [/Biostrings] permanent link Rintact version bump [/Rintact] permanent link Ringo added more checks to plotting functions; added arguments for 'image.RGList' that allow the user to specify what the reporter position dimensions are called in the supplied RGList's 'genes' element (if not 'X' and 'Y') [/Ringo] permanent link annotate Updates the useHomology vignette. This replaces the useHomology vignette with a small vignette that describes how to use the newer inparanoid homology packages. Backed hsahomology and xlahomology out of Depends field in DESCRIPTION file. [/annotate] permanent link explorase Do not treat '#' as comment character when loading data. Set current entity type from type of first file when loading a project (or importing a file). [/explorase] permanent link rHVDM fixing bugs with one of the new functions fixing bugs with one of the new functions fixing bugs with one of the new functions fixing bugs with one of the new functions [/rHVDM] permanent link oligo Adding helper functions for tiling [/oligo] permanent link