CHANGES IN VERSION 1.25.1
------------------------
o add keyType parameter in viewPathway (2018-09-04, Tue)
CHANGES IN VERSION 1.23.2
------------------------
o re-implement viewPathway <2018-03-15, Thu>
o mv site to https://guangchuangyu.github.io/software/ReactomePA
CHANGES IN VERSION 1.23.1
------------------------
o import enrichplot
CHANGES IN VERSION 1.21.3
------------------------
o new project site using blogdown <2017-09-30, Fri>
CHANGES IN VERSION 1.21.2
------------------------
o correct typo in vignette <2017-05-18, Thu>
CHANGES IN VERSION 1.21.1
------------------------
o update vignette according to the change of reactome.db (pathway ID was changed) <2017-04-28, Fri>
CHANGES IN VERSION 1.20.0
------------------------
o BioC 3.5 release <2017-04-26, Wed>
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>