CHANGES IN VERSION 1.5.1 ------------------------ o import ggtitle from ggplot2 <2012-09-07, Fri> o update codes of plot functions accompaning with ggplot2 (version 0.9.2) <2012-09-06, Thu> o bug fixed of buildGOmap due to the empty GO annotation query from biomaRt <2012-07-18, Wed> Changes IN VERSION 1.5.0 ------------------------ o bump up version to 1.5.0 for BioC 2.11 devel o add URL in DESCRIPTION o update citation and add biocView GeneSetEnrichment <2012-05-09, Wed> o support zebrafish <2012-05-18, Mon> CHANGES IN VERSION 1.3.15 ------------------------ o add support to organsims other than human, mouse, and yeast. <2012-03-22, Thu> o add GFFparser.R, which provide function Gff2GeneTable to parse Gff files and build gene information table.<2012-03-22, Thu> o add function buildGOmap for building GO mapping files for unsurported organisms, which can be analyzed now. <2012-03-22, Thu> o add vignette explaining how to run GO analysis for unsupported organism. <2012-03-12, Thu> CHANGES IN VERSION 1.3.14 ------------------------ o re-implement enrichGO by import enrich.internal in DOSE implement S3 methods for mapping IDs for GO analysis. <2012-03-18, Sun> o re-implement enrichKEGG by import enrich.internal in DOSE implement S3 methods for mapping IDs for KEGG analysis. <2012-03-19, Mon> o re-implement groupGOResult class by extended from enrichResult, and modified groupGO by using S3 methods designed for enrichGO. <2012-03-19,Mon> o bug fixed for importing setReadable<- instead of setReadable. <2012-03-20, Tue> o bug fixed of TERM2NAME.GO. <2012-03-21, Wed> CHANGES IN VERSION 1.3.13 ------------------------ o import plot summary from stats4, for BiocGenerics (version 0.1.10) removed them <2012-03-03, Sat> CHANGES IN VERSION 1.3.12 ------------------------ o fixed BibTeX database file .bib. month = , must be month = someMonth, or totally deleted, leave it blank will cause texi2dvi failed. <2012-03-01, Thu> CHANGES IN VERSION 1.3.11 ------------------------ o update vignette. <2012-02-28, Tue> CHANGES IN VERSION 1.3.10 ------------------------ o fixed warnings concerning documents of plot generics. <2012-02-27, Mon> o import summary generic from BiocGenerics instead of stats4. <2012-02-27, Mon> CHANGES IN VERSION 1.3.9 ------------------------ o fixed build error in bioc repos <2012-02-26 Sun> CHANGES IN VERSION 1.3.8 ------------------------ o add visualization section in vignette <2012-02-16 Thu> CHANGES IN VERSION 1.3.7 ------------------------ o @exportMethod plot <2012-02-15 Wed> o fix bug when calling summary method from plot, for summary defined in base is S3 method, instead import summary generic from stats4 <2012-02-15 Wed> CHANGES IN VERSION 1.3.6 ------------------------ o remove generic definition of show, summary and plot, add NAMESPACE import show from methods and plot from graphics. summary need not to import, for is defined in the base package. <2012-02-13 Mon> o rewrite vignette <2012-02-13 Mon> CHANGES IN VERSION 1.3.5 ------------------------ o update plot codes accompany with new version of ggplot2(>=0.9.0) <2012-02-07 Tue> CHANGES IN VERSION 1.3.4 ------------------------ o using apply instead of mdply to improve speed <2012-02-03 Fri> o add citation of clusterProfiler <2012-02-03 Fri> CHANGES IN VERSION 1.3.3 ------------------------ o add showCategory parameter for plot functions <2011-01-11 Wed> CHANGES IN VERSION 1.3.2 ------------------------ o add qvalueCutoff parameter. <2011-01-05 Thu> CHANGES IN VERSION 1.3.1 ------------------------ o add plot.categoryNet for enrichGOResult. <2011-11-10 Thu> CHANGES IN VERSION 1.1.22 ------------------------ o update vignette. <2011-07-23 Thu> CHANGES IN VERSION 1.1.21 ------------------------ o update roxygen docs. <2011-07-23 Sat> CHANGES IN VERSION 1.1.20 ------------------------ o update roxygen docs. <2011-07-19 Wed> CHANGES IN VERSION 1.1.19 ------------------------ o change to using roxygen for generating Rd file. <2011-07-19 Tue> CHANGES IN VERSION 1.1.18 ------------------------ o clean up some codes. <2011-07-19 Tue> CHANGES IN VERSION 1.1.17 ------------------------ o Remove dependence of GOstats and Category. <2011-07-18 Mon> CHANGES IN VERSION 1.1.16 ------------------------ o Re-implement function enrichGO. <2011-07-18 Mon> o add parameter readable, for mapping gene IDs to gene names. <2011-07-18 Mon> CHANGES IN VERSION 1.1.15 ------------------------ o Modified plot method of groupGOResult, with colour coded. <2011-06-15 Wed>