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.	Wed, 09 Apr 2008 arrayQuality AP:modified qualFunc.R: new names for qc measures; changed MmRef and HsRef to proper rownames; remove the varRepA line; fixed some typos in help files [/arrayQuality] permanent link occugene Bumped the version number for the BioC 2.2 release. Also made some minor edits to help files. [/occugene] permanent link flowCore Added a few sentences about Gating-ML and fixed some typos in the text. [/flowCore] permanent link Ringo added another way of estimating the threshold for probe levels under ChIP-enrichment as suggested by Richard Bourgon [/Ringo] permanent link codelink 1.7.5 - added new function c2e to better convert Codelink-objects to CodelinkSet. - c2e accepts a phenoData object (like those read by read.AnnotatedDataFrame(). [/codelink] permanent link SAGx correction to JT.test rd [/SAGx] permanent link flowUtils fixed warnings [/flowUtils] permanent link flowQ bumping version number fixed the NAMESPACE because importing flowCore produced a long list of warnings [/flowQ] permanent link affxparser CPP code for parsing CHP tiling arrays code of the parsing chp files [/affxparser] permanent link xps update to version xps-0.99.8 - update functions root.xxx to work with WinXP - update Makefile clean - update examples/script4xps.R [/xps] permanent link Category updated version [/Category] permanent link xcms Rework file name computation in xcmsSet(). Fix missing symbol in profileMatrix<-(). Cleanup mzClust code [/xcms] permanent link XDE bumped version added documenation for calculatePosteriorAvg added documentation. Documentation for delta_gp model in the XdeParameterClass vignette is still needed [/XDE] permanent link VanillaICE calls.ICE should be working now. updated vignettes [/VanillaICE] permanent link ppiStats i have added the separateExptBySize func [/ppiStats] permanent link Biobase Try to recover more gracefully (suggesting updateObject) when mis-spelt dimLabels discovered eSet AnnotatedDataFrame created with 'featureColumns' spelt incorrectly NEWS from previous change to combine [/Biobase] permanent link