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 GGexplorer GGtools GLAD GOstats GSEABase GSEAlm GeneMeta GeneR GeneRfold GeneSelector GeneSpring GeneTraffic GeneticsBase GeneticsDesign GeneticsPed GenomeGraphs GlobalAncova GraphAT GraphAlignment HELP HEM Harshlight Heatplus HilbertCurveDisplay IRanges 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 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 arrayQuality arrayQualityMetrics beadarray beadarraySNP bgafun bgx bioDist biocGraph biocViews biomaRt bridge buildBioC cellHTS cellHTS2 cghMCR clusterStab codelink convert copa cosmo cosmoGUI ctc daMA diffGeneAnalysis domainsignatures 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, 19 Apr 2008 GGtools out to base ok various changes to depend on GGBase pasing check old file [/GGtools] permanent link flowClust modified namespace - not to import the curv2filter, curv1filter and quadGate classes from flowCore for compatibility with previous versions of flowCore modified namespace - import only relevant classes and methods instead of the whole namespace from flowCore [/flowClust] permanent link oligoClasses Adding JPG for diagram [/oligoClasses] permanent link arrayQuality AP: fixed bug in qcScore and updated help file [/arrayQuality] permanent link GGBase it installs [/GGBase] permanent link GSEABase Update unit tests to match new annotation packages - future goal: make unit tests more independent of specific maps [/GSEABase] permanent link genefilter bumped up to 1.18 [/genefilter] permanent link Biostrings Added basic support for Position Weight Matrix matching thru the new matchPWM() and countPWM() functions. Also added related utility functions maxWeights(), maxScore() and PWMscore(). See ?matchPWM for the details. Bumped version to 2.7.47. Minor edits to the description and details section of the man file. Disabled update() of NormalIRanges objects and fixed a small problem with the "update" method for IRanges objects. Added "isEmpty", "max" and "min" methods for IRanges/NormalIRanges objects. Disabled subsetting and narrowing of NormalIRanges objects (these operations do NOT preserve normality in general). Small improvement to the "gaps" semantic and implementation. [/Biostrings] permanent link sscore Updated vignette to correct spacing problems [/sscore] permanent link PCpheno fix getDescr() to handle deprecated GO terms [/PCpheno] permanent link lumi update lumi vignette [/lumi] permanent link prada added alias to documentation to get rid of warning message during R CMD checK [/prada] permanent link xcms Fixed plotScan() for last spectrum, catch out-of-bounds arguments Increased "max" parameter of group() from 5 to 50 [/xcms] permanent link SLGI fix iSummary to handle deprecated GO terms [/SLGI] permanent link oligo Adding some power user functions [/oligo] permanent link