Bioconductor Changelog

Bioconductor Changelog

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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, 27 Feb 2008 tkWidgets Replaced reference of soon to be defunct class exprSet with ExpressionSet. [/tkWidgets] permanent link siggenes Removed support for soon to be defunct class exprSet. [/siggenes] permanent link safe Made the two changes: 1) Replaced usage of the soon to be deprecated class exprSet with ExpressionSet. 2) Replaced logical T's and F's with TRUEs and FALSEs. [/safe] permanent link puma Removed support for soon to be defunct class exprSet. [/puma] permanent link topGO Replaced reference to soon to be defunct class exprSet with ExpressionSet. [/topGO] permanent link annaffy Replaced references to soon to be defunct class exprSet with ExpressionSet. [/annaffy] permanent link twilight Removed support for soon to be defunct class exprSet. [/twilight] permanent link lapmix Removed support for soon to be defunct class exprSet. [/lapmix] permanent link GeneTraffic Replaced usage of soon to be defunct class exprSet with ExpressionSet. [/GeneTraffic] permanent link ctc Replaced reference to soon to be defunct exprSet class with ExpressionSet. [/ctc] permanent link RMAGEML Replaced usage of soon to be defunct class exprSet with ExpressionSet. [/RMAGEML] permanent link edd Replaced reference to soon to be defunct class exprSet with ExpressionSet. [/edd] permanent link TypeInfo Replaced reference to soon to be defunct class exprSet with ExpressionSet in test script. [/TypeInfo] permanent link geneRecommender Replace usage of soon to be defunct class exprSet with ExpressionSet. [/geneRecommender] permanent link Biostrings Added the chartr() generic function with a method for BString objects. Methods for other types of objects (in particular for BStringViews and BStringSet objects) will come later. Version bump. Versatile constructor RNAString() (resp. DNAString()) now converts from DNA to RNA (resp. RNA to DNA) by replacing T by U (resp. U by T) instead of trying to mimic transciption. This conversion is still performed without copying the sequence data and thus remains very fast. Also the semantic of comparing RNA with DNA has been changed to remain consistent with the new semantic of RNAString() and DNAString() e.g. RNAString("UUGAAAA-CUC-N") is considered equal to DNAString("TTGAAAA-CTC-N"). Version bumped to 2.7.26 [/Biostrings] permanent link clusterStab Removed support for soon to be defunct class exprSet. [/clusterStab] permanent link macat Replaced usage of soon to be defunct class exprSet with ExpressionSet. [/macat] permanent link panp Removed support for soon to be defunct class exprSet. [/panp] permanent link adSplit Made the following three changes: 1) Removed support for soon to be defunct exprSet class. 2) Cleaned up help files for Sv3 methods. 3) Added formal imports of image and hist from the graphics package. [/adSplit] permanent link copa Removed support for soon to be defunct class exprSet. [/copa] permanent link Ringo Removed support for soon to be defunct class exprSet. [/Ringo] permanent link MergeMaid Removed support for soon to be defunct class exprSet. [/MergeMaid] permanent link codelink Changed reference in a vignette from exprSet to ExpressionSet since exprSet is soon to be defunct. [/codelink] permanent link ArrayExpress Set the arguments of download.file and extract.zip so that it works under Windows [/ArrayExpress] permanent link BufferedMatrixMethods (1.3.4) Make minor changes to what is printed to the screen when verbose=TRUE in BufferedMatrix.read.probematrix() and BufferedMatrix.justRMA() [/BufferedMatrixMethods] permanent link pgUtils Removed comments with reference to soon to be defunct class exprSet. [/pgUtils] permanent link OrderedList Removed reference to soon to be defunct class exprSet from code comment. [/OrderedList] permanent link explorase Make Refresh button insensitive after refresh. Make capitalization consistent in Limma front-end. Make backwards compatible with non-csv suffixed files. Clicking on a node in the ggtree now brushes the descendent leaves. Use .csv as final extension for lists, info, data and design. Disable 'Find' button in 'Find Patterns' until 'Refresh' is pressed after the cutoff has been adjusted. Add 'cor-p-values' output option for outputting the corrected p-values. FDR is now the default p-value correction method. [/explorase] permanent link ABarray Made two changes: 1) Replaced usage of soon to be defunct class exprSet with ExpressionSet. 2) Replaced logicals T's and F's with TRUEs and FALSEs. [/ABarray] permanent link AffyExpress Replaced reference of soon to be defunct class exprSet with ExpressionSet. [/AffyExpress] permanent link xps update to version xps-0.5.0 - eliminated memory leaks in C++ code parsing generic CEL-files - C++ source code can now be compiled with MS Visual C++ [/xps] permanent link maSigPro Replaced a call to the deprecated read.exprSet function with readExpressionSet. [/maSigPro] permanent link geneplotter Fixed a bug in densCols which caused a mismapping of colors to points [/geneplotter] permanent link XDE This adds the new package XDE to the bioconductor repository. [/XDE] permanent link exonmap Replace support for soon to be defunct class exprSet with ExpressionSet. [/exonmap] permanent link idiogram Changed support from exprSet to ExpressionSet as the former class will soon be defunct. [/idiogram] permanent link metaArray Replaced usage of soon to be defunct class exprSet with ExpressionSet. [/metaArray] permanent link GraphAlignment This adds the new GraphAlignment package to the repository. [/GraphAlignment] permanent link Biobase Fixed a typo in the deprecation message. [/Biobase] permanent link