CHANGES IN VERSION 2.3.1 ------------------------ o new project site using blogdown <2017-09-28, Thu> o speed up by pre-calculating GO similarities <2017-05-22, Mon> + contributed by Lluís Revilla Sancho + https://github.com/GuangchuangYu/GOSemSim/pull/13 CHANGES IN VERSION 2.2.0 ------------------------ o BioC 3.5 release <2017-04-26, Wed> CHANGES IN VERSION 2.1.3 ------------------------ o friendly error message for using IC method without IC computed <2017-02-17, Fri> + https://github.com/GuangchuangYu/GOSemSim/issues/11 o fixed https://github.com/GuangchuangYu/GOSemSim/issues/9 <2016-12-20, Tue> CHANGES IN VERSION 2.1.2 ------------------------ o use prettydoc for vignette <2016-11-30, Wed> o remove using BiocStyle <2016-11-23, Wed> CHANGES IN VERSION 2.1.1 ------------------------ o update startup message <2016-11-09, Wed> CHANGES IN VERSION 2.0.0 ------------------------ o BioC 3.4 released <2016-10-18, Tue> CHANGES IN VERSION 1.99.4 ------------------------ o fixed NOTE in R check <2016-08-12, Fri> o add unit test using testthat <2016-08-11, Thu> CHANGES IN VERSION 1.99.3 ------------------------ o changes to satisfy meshes package <2016-08-05, Fri> CHANGES IN VERSION 1.99.2 ------------------------ o fixed Rcpp issue <2016-07-19, Tue> + https://github.com/GuangchuangYu/GOSemSim/issues/6 CHANGES IN VERSION 1.99.1 ------------------------ o update vignette <2016-07-14, Thu> CHANGES IN VERSION 1.99.0 ------------------------ o support all organisms that have OrgDb object <2016-07-05, Tue> o optimize Wang method <2016-07-04, Mon> CHANGES IN VERSION 1.31.2 ------------------------ o use byte compiler <2016-05-18, Wed> o https://github.com/Bioconductor-mirror/GOSemSim/commit/71c29280c560e0293569121aeeecb0ed7b37055a CHANGES IN VERSION 1.31.1 ------------------------ o https://github.com/Bioconductor-mirror/GOSemSim/commit/a829a50a017b90f08c41b5955df176dfad333d06 CHANGES IN VERSION 1.30.0 ------------------------ o BioC 3.3 released <2016-05-05, Thu> CHANGES IN VERSION 1.29.2 ------------------------ o update IC data <2016-04-21, Mon> CHANGES IN VERSION 1.29.1 ------------------------ o fixed R check <2016-03-05, Sat> CHANGES IN VERSION 1.27.4 ------------------------ o update information content data <2015-10-08, Thu> o convert vignette from Rnw to Rmd <2015-06-23, Tue> CHANGES IN VERSION 1.27.3 ------------------------ o bug fixed in getSupported_Org <2015-05-31, Sun> CHANGES IN VERSION 1.27.2 ------------------------ o deprecate 'worm' and use 'celegans' instead. CHANGES IN VERSION 1.27.1 ------------------------ o add external documents <2015-05-07, Thu> CHANGES IN VERSION 1.25.5 ------------------------ o update information content files <2015-03-12, Thu> CHANGES IN VERSION 1.25.4 ------------------------ o update vignette and add DOSE citation <2015-02-13, Fri> CHANGES IN VERSION 1.25.3 ------------------------ o add doi in CITATION <2015-01-28, Wed> o update vignette using BiocStyle <2015-01-26, Mon> CHANGES IN VERSION 1.25.2 ------------------------ o add BugReports URL <2014-12-17, Wed> CHANGES IN VERSION 1.25.1 ------------------------ o import Rcpp <2014-10-23, Thu> CHANGES IN VERSION 1.23.2 ------------------------ o fast IC-method implemented, contributed by Alexey Stukalov <2014-09-27, Sat> CHANGES IN VERSION 1.23.1 ------------------------ o add support of species coelicolor and gondii <2014-09-03, Wed> CHANGES IN VERSION 1.21.3 ------------------------ o fixed minor bug in combineMethods <2013-12-16, Mon> CHANGES IN VERSION 1.19.3 ------------------------ o add getSupported_Org function for accessing all the names of supported organisms <2013-07-09, Mon> CHANGES IN VERSION 1.19.2 ------------------------ o export getDb and loadGOMap <2013-07-09, Mon> o update vignettes <2013-07-9, Mon> CHANGES IN VERSION 1.19.1 ------------------------ o update vignettes <2013-06-13, Thu> CHANGES IN VERSION 1.17.1 ------------------------ o update IC data for next release <2013-03-08, Fri> o after removing NA row/col of similarity matrix, if only one row/col remains, R will turn it to be a vector, and combineScore function will not work properly. This bug was fixed <2013-01-11, Fri> o bug fixed of infoContentMethod, now return NA when ID is not belong to the ontology <2012-10-11, Thu> CHANGES IN VERSION 1.15.3 ------------------------ o remove all the S4 classes and methods <2012-09-12, Wed> o add progress bar for mgeneSim <2012-09-12, Wed> o re-implement calculating semantic values in Wang's method <2012-09-12, Wed> o update IC data for next release <2012-09-12, Wed> o bug fixed in getSV <2012-09-13, Thu> CHANGES IN VERSION 1.15.2 ------------------------ o re-implement gene2GO <2012-09-7, Fri> o information content based methods implemented in c++ <2012-09-5, Wed> CHANGES IN VERSION 1.15.1 ------------------------ o export termSim, which can be used in other ontological semantic similarity measurement <2012-06-14, Thu> o update vignette. <2012-06-14, Thu> CHANGES IN VERSION 1.13.6 ------------------------ o remove dependency of organism annotation packages. <2012-03-09, Fri> User not need to install all these annotation packages for using GOSemSim. User only need to install the specific organism annotation package they want to calculate. o update IC data sets for 1.14 release. <2012-03-30, Fri> CHANGES IN VERSION 1.13.5 ------------------------ o fixed BibTeX database file .bib. month = , must be month = someMonth, leave it blank will cause texi2dvi failed. <2012-03-01, Thu> CHANGES IN VERSION 1.13.4 ------------------------ o update vignette. <2012-02-28, Tue> CHANGES IN VERSION 1.13.3 ------------------------ o bug fixed for multiple annotation. <2012-02-01, Fri> CHANGES IN VERSION 1.13.2 ------------------------ o update infoContentMethod to make it consistent between DOSE and GOSemSim. <2011-12-31, Sat> CHANGES IN VERSION 1.13.1 ------------------------ o remove dependency of DOSE o remove Streptomyces coelicolor support, as the genome wide annotation package contributor no longer supports it. CHANGES IN VERSION 1.11.2 ------------------------ o Using methods implemented in DOSE for semantic similarity calculation.