CHANGES IN VERSION 1.99.0 ------------------------ o set version to 1.99.0 and will release version 2.0.0 in next BioConductor release. <2014-09-03, Wed> + In version 2.0.0, the package was extended to support about 20 species for both of GO and KEGG analyses. + support gene set enrichment analysis algorithm for both of GO and KEGG. + support enrichMap visualization. o support about 20 species of KEGG analyses. <2014-09-03, Wed> o update man file to indicate that enrichGO is now support more than 20 species <2014-09-03, Wed> CHANGES IN VERSION 1.13.3 ------------------------ o add keepGOlevel, keepGOterm, excludeGOlevel, excludeGOterm, not exported yet <2014-08-28, Thu> CHANGES IN VERSION 1.13.2 ------------------------ o implement gseGO and gseKEGG for gene set enrichment analysis <2014-07-31, Thu> o import enrichMap from DOSE <2014-07-31, Thu> o add corresponding section in vignettes <2014-07-31, Thu> CHANGES IN VERSION 1.13.1 ------------------------ o update man files according to the change of roxygen2 (ver 4.0.0) <2014-05-16, Fri> CHANGES IN VERSION 1.11.3 ------------------------ o now plotting compareClusterResult support scale the dot size by geneRatio, and it is now setting as default. <2014-01-14, Tue> o The original default parameter by="percentage" is now changing to "rowPercentage" <2014-01-14, Tue> CHANGES IN VERSION 1.11.2 ------------------------ o remove viewKEGG function <2013-11-12, Tue> o In vignette, illustrates how to visualize KEGG pathway using use pathview package. <2013-11-12, Tue> CHANGES IN VERSION 1.9.4 ------------------------ o bug fixed of readGff, add default parameter fill=TRUE in read.table function <2013-07-09, Mon> CHANGES IN VERSION 1.9.3 ------------------------ o extend enrichGO to support 20 species <2013-07-09, Mon> o update vignettes. <2013-07-09, Mon> CHANGES IN VERSION 1.9.1 ------------------------ o enrichGO and enrichKEGG support rat organism <2013-05-20, Mon> o change some code according to DOSE <2013-03-27, Wed> o modify enrichGO and enrichKEGG according to the change of enrich.internal, remove qvalueCutoff parameter, add pAdjustMethod, add universe paramter for user to specify background. <2013-05-29, Wed> o add function viewKEGG for visualizing KEGG pathway and update vignette. <2013-06-14, Fri> CHANGES IN VERSION 1.7.1 ------------------------ o support GO enrichment analysis for organism celegans <2013-01-22, Fri> o add compress parameter in buildGOmap <2013-01-16, Wed> 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>