CHANGES IN VERSION 1.19.1 ------------------------ o update startup message <2016-11-09, Wed> CHANGES IN VERSION 1.18.0 ------------------------ o BioC 3.4 released <2016-10-18, Tue> CHANGES IN VERSION 1.17.4 ------------------------ o unit test <2016-08-15, Mon> CHANGES IN VERSION 1.17.3 ------------------------ o move getDb from GOSemSim (no longer need this function) to ReactomePA and remove dependency of GOSemSim <2016-07-06, Wed> o 'by' parameter for GSEA analysis <2016-07-04, Mon> CHANGES IN VERSION 1.17.2 ------------------------ o use byte compiler <2016-05-18, Wed> o https://github.com/Bioconductor-mirror/ReactomePA/commit/6ce32c8e03e1b252662a07901cce022fab038086 CHANGES IN VERSION 1.17.1 ------------------------ o https://github.com/Bioconductor-mirror/ReactomePA/commit/5d150f5fe545cfa3983872bf5485af1b9ba3129d CHANGES IN VERSION 1.16.0 ------------------------ o BioC 3.3 released <2016-05-05, Thu> CHANGES IN VERSION 1.15.6 ------------------------ o fixed issue of duplicated name in PATHID2NAME <2016-04-21, Thu> CHANGES IN VERSION 1.15.5 ------------------------ o add maxGSSize parameter <2016-03-10, Thu> o update ReactomePA citation info <2016-02-17, Wed> CHANGES IN VERSION 1.15.4 ------------------------ o according to the update of DOSE <2015-12-20, Sun> CHANGES IN VERSION 1.15.3 ------------------------ o update citation info <2015-11-24, Tue> CHANGES IN VERSION 1.15.2 ------------------------ o update vignette <2015-11-16, Mon> CHANGES IN VERSION 1.15.1 ------------------------ o update vignette <2015-10-28, Wed> CHANGES IN VERSION 1.14.0 ------------------------ o BioC 3.2 Branch CHANGES IN VERSION 1.13.5 ------------------------ o add support of fly (Drosophila melanogaster) <2015-09-22, Tue> CHANGES IN VERSION 1.13.4 ------------------------ o update vignette <2015-08-19, Wed> CHANGES IN VERSION 1.13.3 ------------------------ o add citation of ChIPseeker <2015-07-09, Thu> o add 'Pathway analysis of NGS data' section in vignette <2015-06-29, Mon> o convert vignette from Rnw to Rmd <2015-06-29, Mon> CHANGES IN VERSION 1.13.2 ------------------------ o enable other organisms for viewPathway by Vladislav Petyuk <2015-05-28, Thu> see https://github.com/GuangchuangYu/ReactomePA/pull/1 CHANGES IN VERSION 1.13.1 ------------------------ o update enrichMap and viewPathway <2015-05-13, Wed> CHANGES IN VERSION 1.11.9 ------------------------ o use mapIds instead of mget in TERM2NAME. mapIds will not throw error when pathID is old/deprecated. <2015-04-10, Fri> CHANGES IN VERSION 1.11.8 ------------------------ o according to https://support.bioconductor.org/p/63024/#66438, modify gsePathway to only test pathways. <2015-04-09, Thu> CHANGES IN VERSION 1.11.7 ------------------------ o update use_internal_data parameter to ... according to the change of DOSE <2015-04-01, Wed> CHANGES IN VERSION 1.11.6 ------------------------ o update according to DOSE <2015-03-31, Tue> add use_internal_data parameter in internal functional of enrichPathway. CHANGES IN VERSION 1.11.5 ------------------------ o update according to DOSE <2015-03-01, Sun> add use_internal_data parameter in getGeneSet. CHANGES IN VERSION 1.11.2 ------------------------ o remove import org.Hs.eg.db <2015-01-22, Thu> CHANGES IN VERSION 1.11.1 ------------------------ o fix some pathways don't have a name <2014-11-17, Mon> ## > get("5493857", reactomePATHID2EXTID) ## [1] "510850" "523328" "282187" "282188" ... ## > get("5493857", reactomePATHID2NAME) ## Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : ## value for "5493857" not found --> This is not a bug in ReactomePA, but an issue of reactome.db, refer to: --> https://support.bioconductor.org/p/63024/ CHANGES IN VERSION 1.9.4 ------------------------ o add gseaplot function <2014-07-31, Thu> CHANGES IN VERSION 1.9.3 ------------------------ o import enrichMap from DOSE <2014-07-31, Thu> CHANGES IN VERSION 1.9.2 ------------------------ o update roxygen to version 4 <2014-06-09, Mon> CHANGES IN VERSION 1.9.1 ------------------------ o bug fixed of TERM2NAME.Reactome <2014-04-21, Mon> CHANGES IN VERSION 1.7.2 ------------------------ o bug fixed for multi-organisms support <2013-12-09, Mon> CHANGES IN VERSION 1.5.3 ------------------------ o bug fixed in TERMID2EXTID <2013-09-18, Wed> CHANGES IN VERSION 1.5.2 ------------------------ o implement gseAnalyzer for GSEA analysis <2013-07-10, Wed> o implement viewPathway for visualizing pathway <2013-07-10, Wed> CHANGES IN VERSION 1.5.1 ------------------------ o extend enrichPathway to support rat, mouse, celegans, zebrafish, and fly. <2013-03-27, Wed> o modify enrichPathway according to the change of enrich.internal, remove qvalueCutoff parameter, add pAdjustMethod, add universe paramter for user to specify background. <2013-05-29, Wed> CHANGES IN VERSION 1.3.1 ------------------------ o bug fixed of ALLEXTID. <2013-03-1, Fri> CHANGES IN VERSION 1.1.1 ------------------------ o remove geneID2Name, instead import EXTID2NAME from DOSE. <2012-03-12, Mon> o remove most of the codes in enrichPathway, instead import enrich.internal in DOSE. implement some S3 method for mapping. pathID2Name was rename to TERM2NAME, which will called by enrich.internal. <2012-03-12, Tue> CHANGES IN VERSION 0.99.0 ------------------------ o change package name to ReactomePA, for there is already an RPA package. <2012-03-02, Fri> o Vignette issues: <2012-03-02, Fri> change image format from .eps to .pdf, make it easier to build. remove the tolatex tag of sessionInfo(), make the output more readble. o re-implement geneID2Name using select method. <2012-03-02, Fri> o add examples in man pages. <2012-03-02, Fri> o remove man pages of internal functions. <2012-03-02, Fri> o import plot summary from stats4, for BiocGenerics (version 0.1.10) removed them <2012-03-03, Sat> o add Methods section in enrichPathwayResult-class man page. <2012-03-05, Mon> CHANGES IN VERSION 0.2.3 ------------------------ 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 0.2.2 ------------------------ 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 <2012-02-10 Fri> CHANGES IN VERSION 0.2.1 ------------------------ o update vignette <2012-02-09 Thu> o add sample data (an example list of genes from ProfCom: http://webclu.bio.wzw.tum.de/profcom/gene_Lists/example1.txt the gene symbols were converted to entrezgene) <2012-02-09 Thu> CHANGES IN VERSION 0.2.0 ------------------------ o separate codes of mapping pathway ID to pathway Name to a new function pathID2Name <2012-02-09 Thu> o implement geneID2Name function for mapping gene ID to gene Symbol <2012-02-09 Thu> o add parameter readable in function enrichPathway <2012-02-09 Thu> o implement cnetplot for plotting category net <2012-02-09 Thu> o modify plot function for class enrichPathwayResult to use cnetplot <2012-02-09 Thu> CHANGES IN VERSION 0.1.1 ------------------------ o add vignette <2012-02-08 Wed> o bug fixed for multiple mapping of pathway ID to pathway Name such as pathway 162906 can mapping to 1629061 and 1629062 when getting pathway name, remain the first one. <2012-02-08 Wed> CHANGES IN VERSION 0.1.0 ------------------------ o implement show, summary and plot method for enrichPathwayResult class <2012-02-08 Wed> o define class enrichPathwayResult to store result of enrichPathway <2012-02-08 Wed> o implement enrichPathway function for enrichment analysis. using hypergeometric model <2012-02-08 Wed> o initial package skeleton <2012-02-08 Wed>