CHANGES IN VERSION 2.8.1
------------------------
o produced more conserved p-values for GSEA <2015-10-28, Wed>
CHANGES IN VERSION 2.7.12
------------------------
o output a list of data frames by enrichMap via invisible, so that the graph info can be viewed by other tools, eg. Cytoscape. <2015-09-30, Wed>
CHANGES IN VERSION 2.7.11
------------------------
o check whether input geneList is sorted <2015-09-22, Tue>
o order first followed by showCategory subsetting in barplot <2015-09-08, Tue>
+ https://support.bioconductor.org/p/71917/#71939
o bug fixed in EXTID2NAME, keytype is TAIR for arabidopsis and ORF for malaria <2015-08-26, Wed>
CHANGES IN VERSION 2.7.10
------------------------
o add Giovanni Dall'Olio as contributor in author list. <2015-07-21, Tue>
o update NCG data to version cancergenes_4.9.0_20150720 contributed by Giovanni Dall'Olio.
https://github.com/GuangchuangYu/DOSE/pull/8 <2015-07-21, Tue>
o geneInCategory may simplify to vector by R in very rare case,
which violate the assumption of list in S4 validation checking.
This issue was fixed. <2015-07-19, Sun>
CHANGES IN VERSION 2.7.9
------------------------
o add citation of ChIPseeker <2015-07-09, Thu>
o add 'Disease analysis of NGS data' section in vignette <2015-06-29, Mon>
o convert vignette from Rnw to Rmd <2015-06-24, Wed>
CHANGES IN VERSION 2.7.8
------------------------
o dotplot for enrichResult <2015-06-21, Sun>
CHANGES IN VERSION 2.7.7
------------------------
o speed up by using sample.int instead of sample <2015-06-04, Thu>
o add seed = FALSE to control reproduciblility of gsea function.
to make result reproducible, explicitly set seed=TRUE <2015-06-04, Thu>
- contributed by Vlad, see https://github.com/GuangchuangYu/DOSE/pull/5/
- modified by Guangchuang
CHANGES IN VERSION 2.7.6
------------------------
o bug fixed in cnetplot legend contributed by Vladislav Petyuk <2015-05-28, Thu>
CHANGES IN VERSION 2.7.5
------------------------
o update vignette <2015-05-15, Fri>
CHANGES IN VERSION 2.7.4
------------------------
o update permutation test with pvalue = (K+1)/(N+1) instead of K/N,
so that p value will never be 0 <2015-05-12, Tue>
CHANGES IN VERSION 2.7.3
------------------------
o add setType slot in gseaResult <2015-05-15, Tue>
o add universe and geneSets slots in enrichResult <2015-05-05, Tue>
CHANGES IN VERSION 2.7.2
------------------------
o add vertex.label.font parameter in enrichMap <2015-04-27, Mon>
CHANGES IN VERSION 2.7.1
------------------------
o update NCG description in enrichNCG <2015-04-22, Wed>
CHANGES IN VERSION 2.5.12
------------------------
o report NA in qvalue column when it fail to calculate instead of throw error <2015-03-09, Thu>
o update IC data <2015-03-08, Wed>
CHANGES IN VERSION 2.5.11
------------------------
o implement clusterSim and mclusterSim <2015-03-07, Tue>
CHANGES IN VERSION 2.5.10
------------------------
o implement enrichNCG and now gseAnalyzer accept setType = "NCG" <2015-04-01, Wed>
see http://ncg.kcl.ac.uk
o change use_internal_data parameter to ... in all S3 generics and methods <2015-04-01, Wed>
CHANGES IN VERSION 2.5.9
------------------------
o extend gseAnalyzer to support use_internal_data parameter <2015-03-29, Sun>
CHANGES IN VERSION 2.5.8
------------------------
o keep order of barplot, sorted by pvalue by defalt <2015-02-11, Wed>
CHANGES IN VERSION 2.5.7
------------------------
o fixed typo in vignette <2015-02-10, Tue>
CHANGES IN VERSION 2.5.6
------------------------
o add organismMapper to satisfy the change of enrichKEGG <2015-01-28, Wed>
CHANGES IN VERSION 2.5.5
------------------------
o introduce use_internal_data parameter for enrichKEGG of clusterProfiler <2015-01-27, Tue>
CHANGES IN VERSION 2.5.3
------------------------
o update vignette <2015-01-27, Tue>
CHANGES IN VERSION 2.5.1
------------------------
o add CITATION <2015-01-19, Mon>
CHANGES IN VERSION 2.3.6
------------------------
o add readable parameter in simplot <2014-10-09, Thu>
CHANGES IN VERSION 2.3.5
------------------------
o implement enrichMap <2014-07-28, Wed>
CHANGES IN VERSION 2.3.4
------------------------
o return ggplot2 objects in gseaplot <2014-07-21, Mon>
CHANGES IN VERSION 2.3.3
------------------------
o geneSim can only accept one gene ID vector and perform as mgeneSim in GOSemSim <2014-06-23, Mon>
o update man files <2014-06-23, Mon>
CHANGES IN VERSION 2.3.2
------------------------
o bug fixed in scaleNodeColor <2014-06-08, Sun>
CHANGES IN VERSION 2.3.1
------------------------
o upgrade man file according to roxygen2 (ver 4.0.0) . <2014-05-16, Fri>
CHANGES IN VERSION 1.99.6
------------------------
o bug fixed in EXTID2NAME. <2013-09-28, Sat>
CHANGES IN VERSION 1.99.5
------------------------
o fixed in calculating M when only one categroy presented, the object was matrix insted of list. <2013-09-16, Mon>
CHANGES IN VERSION 1.99.4
------------------------
o export gsea function <2013-07-10, Wed>
CHANGES IN VERSION 1.99.3
------------------------
o extend EXTID2NAME to support 20 species <2013-07-09, Tue>
o update vignette. <2013-07-09, Tue>
CHANGES IN VERSION 1.99.1
------------------------
o convert vignette file to knitr Sweave. <2013-06-24, Mon>
CHANGES IN VERSION 1.99.0
------------------------
o extent ggplot to support enrichResult by implementing fortify method. <2013-05-22, Wed>
o re-implement barplot.enrichResult. <2013-05-23, Thu>
o enrich.internal support user specifiy background by parameter universe. <2013-05-24, Fri>
o implement Gene Set Enrichment Analysis algorithm. <2013-05-29, Wed>
o change setReadable to support groupGO of clusterProfiler. <2013-05-29, Wed>
o fixed mclapply not support Windows platform issue. <2013-05-30, Fri>
o rename logFC parameter to foldChange. <2013-06-13, Thu>
CHANGES IN VERSION 1.7.1
------------------------
o use geom_bar(stat="identity") instead of geom_bar() in barplot for explicitly mapping y value. <2013-05-08, Wed>
o bug fixed when qvalue can't calculated. <2013-05-02, Thu>
o bug fixed of enrich.internal, drop those genes that without annotation when calculating sample gene number. <2013-05-02, Thu>
o change some code to satisfy ReactomePA <2013-03-27, Wed>
CHANGES IN VERSION 1.5.1
------------------------
o bug fixed in enrich.internal, now return NA rather than throw error, if gene have no ontology annotation <2013-01-22, Fri>
CHANGES IN VERSION 1.3.2
------------------------
o update codes of plot functions accompaning with ggplot2 (version 0.9.2) <2012-09-06, Thu>
o update cnetplot corresponding to igraph version 0.6 <2012-07-11, Wed>
o parameter showCategory now support term ID vector <2012-07-11, Wed>
o import termSim and combineScores from GOSemSim. <2012-06,14, Thu>
o optimize setReadable <2012-05-09, Wed>
o bug fixed of setReadable method. For those unmapped genes, return the original gene ID. <2012-05-15, Tue>
o fill color in barplot for Ontology classification. <2012-05-22, Tue>
o update color scale of cnetplot <2012-06-18, Mon>
CHANGES IN VERSION 1.3.1
------------------------
o update color scheme of cnetplot <2012-04-10, Tue>
o add simplot for plotting semantic similarity matrix <2012-04-20, Fri>
o bug fixed of combineScore function for DO semantic similarity matrix
which containing NA rows of NA coloumns <2012-04-20, Fri>
o export doSim and geneSim functions <2012-04-20, Fri>
CHANGES IN VERSION 1.1.12
------------------------
o implement barplot for enrichResult <2012-03-18, Sun>
o bug fixed for setReadable method <2012-03-19, Mon>
o add logFC parameter for cnet plot, support color gene nodes by
their expression value (log fold change) <2012-03-21, Wed>
o add mapping entrezgene ID and gene Name for organisms
other than human, mouse and yeast. <2012-03-22, Thu>
o bug fixed for attempt to name logFC, when it is NULL. <2012-03-22, Thu>
o optimized readable method. <2012-03-26, Mon>
CHANGES IN VERSION 1.1.11
------------------------
o setReadable method for mapping gene ID to gene Symbol in enrichResult instance. <2012-03-12, Mon>
o export method show. <2012-03-12, Mon>
CHANGES IN VERSION 1.1.10
------------------------
o import plot summary from stats4, for BiocGenerics (version 0.1.10) removed them <2012-03-03, Sat>
o Add DO2ALLEG and EG2ALLDO, for mapping undirecte annotation. <2012-03-03, Sat>
o update vignette <2012-03-06, Tue>
CHANGES IN VERSION 1.1.9
------------------------
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>
o update IC data and DO-EG mapping data. <2012-03-01, Thu>
CHANGES IN VERSION 1.1.8
------------------------
o update vignette, add semantic similarity algorithms' details. <2012-02-28, Tue>
CHANGES IN VERSION 1.1.7
------------------------
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 1.1.6
------------------------
o defined S3 generic for ALLEXTID, EXTID2NAME, EXTID2TERMID, TERM2NAME,
and TERMID2EXTID. <2012-02-26, Sun>
o update roxygen and regenerate man file. <2012-02-26, Sun>
o import S4 generics of plot from BiocGenerics. <2012-02-26, Sun>
CHANGES IN VERSION 1.1.5
------------------------
o add S4 method of plot, which accept parameter type = "cnet",
and call cnetplot.enrichResult method. <2012-02-23, Thu>
o add S3 method cnetplot.enrichResult for plotting enrichResult object.
<2012-02-23, Thu>
o define cnetplot function for category-gene network visualization. <2012-02-23, Thu>
o remove generic definition of show and summary,
import show from methods and summary from stats4 <2012-02-23, Thu>
o redefine functions as S3 methods for mapping ID among gene and Term.
this will make enrich.internal which calling these mapping function more robust
<2012-02-23, Thu>
CHANGES IN VERSION 1.1.4
------------------------
o add Enrichment Analysis session in vignette. <2012-02-22, Wed>
o optimize enrichDO, ten time faster. <2012-02-22, Wed>
o separate code of enrichDO to enrich.internal, make it more general,
and can be applied to other ontology. <2012-02-22, Wed>
o rename enrichDOResult class to enrichResult and add slot geneInCategory. <2012-02-22, Wed>
o export infoContentMethod and wangMethod. <2012-02-22, Wed>
CHANGES IN VERSION 1.1.3
------------------------
o update infoContentMethod to make it consistent between DOSE and GOSemSim. <2011-12-31, Sat>
CHANGES IN VERSION 1.1.2
------------------------
o change to using roxygen for generating Rd docs
CHANGES IN VERSION 1.1.1
------------------------
o add function rebuildAnnoData
o update Disease-Gene Mapping data
CHANGES IN VERSION 0.99.7
------------------------
o fixed bug in .SemVal_internal
CHANGES IN VERSION 0.99.6
------------------------
o Use qvalue instead of fdrtool to calculate qvalues.