CHANGES IN VERSION 3.1.3 ------------------------ o output expected sample gene ID when input gene ID type not match <2017-03-27, Mon> o dotplot for gseaResult <2016-11-23, Fri> + https://github.com/GuangchuangYu/DOSE/issues/20 CHANGES IN VERSION 3.1.2 ------------------------ o in gseaplot, call grid.newpage only if dev.interactive() <2016-11-16, Wed> o change minGSSize < geneSet_size & geneSet_size < maxGSSize to minGSSize <= geneSet_size & geneSet_size <= maxGSSize <2016-11-16, Wed> o fixed show method issus of unknown setType in clusterProfiler::GSEA output <2016-11-15, Tue> o throw more friendly error msg if fail to determine setType automatically in setReadable function <2016-11-15, Tue> + https://support.bioconductor.org/p/89445/#89479 o apply minGSSize and maxGSSize to fgsea <2016-11-14, Mon> o change summary to as.data.frame in internal calls to prevent warning message <2016-11-14, Mon> CHANGES IN VERSION 3.1.1 ------------------------ o update startup message <2016-11-09, Wed> o fixed parallel in Windows (not supported) <2016-10-24, Mon> + https://github.com/GuangchuangYu/DOSE/issues/16 o options(DOSE_workers = x) to set using x cores for GSEA analysis is removed. <2016-10-24, Mon> instead let MulticoreParam() to decide how many cores (can be set by `options(mc.cores = x)`). CHANGES IN VERSION 3.0.0 ------------------------ o BioC 3.4 released <2016-10-18, Tue> CHANGES IN VERSION 2.11.12 ------------------------ o deprecate summary method and use as.data.frame instead <2016-09-29, Thu> CHANGES IN VERSION 2.11.11 ------------------------ o export geneID and geneInCategory <2016-09-19, Mon> CHANGES IN VERSION 2.11.10 ------------------------ o geneID and geneInCategory accessor functions <2016-09-19, Mon> CHANGES IN VERSION 2.11.9 ------------------------ o enrichMap works with result contains only one term <2016-08-15, Wed> + https://github.com/GuangchuangYu/DOSE/issues/15 o build_Anno now works with tibble <2016-08-18, Tue> CHANGES IN VERSION 2.11.8 ------------------------ o add unit test <2016-08-15, Mon> CHANGES IN VERSION 2.11.7 ------------------------ o change for meshes packages <2016-08-11, Thu> CHANGES IN VERSION 2.11.6 ------------------------ o user can use options(DOSE_workers = x) to set using x cores for GSEA analysis <2016-08-02, Tue> o support DisGeNET enrichment analyses <2016-08-01, Mon> + enrichDGN, enrichDGNv, gseDGN o update vignettes <2016-07-29, Fri> CHANGES IN VERSION 2.11.5 ------------------------ o enrichMap now output igraph object that can be viewed using other software like networkD3 <2016-07-25, Mon> o dim methods for enrichResult and gseaResult <2016-07-22, Fri> o $ methods for enrichResult and gseaResult <2016-07-20, Wed> o switch from parallel to BiocParallel <2017-07-07, Thu> o [, head and tail methods for enrichResult and gseaResult <2016-07-06, Wed> o change according to GOSemSim <2016-07-05, Tue> CHANGES IN VERSION 2.11.4 ------------------------ o 'title' parameter for gseaplot <2016-07-04, Mon> + contributed by https://github.com/pedrostrusso + https://github.com/GuangchuangYu/DOSE/pull/13 o 'by' parameter in GSEA_internal, by default by = 'fgsea' <2016-07-04, Mon> + by = 'fgsea', use GSEA algorithm implemented in fgsea + by = 'DOSE', use GSEA algorithm implemented in DOSE o leading edge analysis for GSEA <2016-07-04, Mon> CHANGES IN VERSION 2.11.3 ------------------------ o output igraph object in cnetplot <2016-06-21, Tue> o upsetplot generics <2016-06-14, Tue> o [[ methods for enrichResult and gseaResult for accessing gene set <2016-06-14, Tue> CHANGES IN VERSION 2.11.2 ------------------------ o use byte compiler <2016-05-18, Wed> o https://github.com/Bioconductor-mirror/DOSE/commit/6c508c6a6816f465bb372f30f4ab99c839d81767 CHANGES IN VERSION 2.11.1 ------------------------ o https://github.com/Bioconductor-mirror/DOSE/commit/7e87d01e671ce1b5fbe974c06b796b1a2970f11c CHANGES IN VERSION 2.10.0 ------------------------ o BioC 3.3 released <2016-05-05, Thu> CHANGES IN VERSION 2.9.7 ------------------------ o barplot accepts x and colorBy parameters as in dotplot <2016-04-13, Wed> o gsfilter function for restricting result with minimal and maximal gene set size <2016-03-31, Thu> + see https://github.com/GuangchuangYu/clusterProfiler/issues/46 CHANGES IN VERSION 2.9.6 ------------------------ o add maxGSSize parameter for hypergeometric test <2016-03-09, Wed> o add maxGSSize parameter in GSEA analysis. <2016-03-09, Wed> + Default of 500 is fairly standard for GSEA analysis. + Usually if the geneset > 500, its probability of being called significant by GSEA rises quite dramatically. o fixed R check <2016-03-05, Sat> o update ReactomePA citation info <2016-02-17, Wed> CHANGES IN VERSION 2.9.5 ------------------------ o upset plot for enrichResult object <2016-01-22, Fri> CHANGES IN VERSION 2.9.4 ------------------------ o bug fixed in scaling category sizes in enrichMap <2016-01-10, Sun> + use setSize in gseResult CHANGES IN VERSION 2.9.3 ------------------------ o update enrichMap to scale category sizes <2016-01-04, Mon> o update 'show' methods of enrichResult and gseaResult <2015-12-29, Tue> CHANGES IN VERSION 2.9.2 ------------------------ o re-design internal function <2015-12-20, Sun> CHANGES IN VERSION 2.9.1 ------------------------ o GSEA: test bimodal separately <2015-10-28, Wed> o add NES column in GSEA result <2015-10-28, Wed> o use NES instead of ES in calculating p-values. <2015-10-28, Wed> o duplicated gene IDs in enrich.internal is not allow. add `unique` to remove duplicated ID. <2015-10-20, Tue> + see https://github.com/GuangchuangYu/clusterProfiler/issues/27 CHANGES IN VERSION 2.9.0 ------------------------ o BioC 3.3 branch 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.