CHANGES IN VERSION 2.8.0 ---------------------- NEW FEATURES o New function getListGIF is added to interact with ListGIF web server (http://listgif.nubic.northwestern.edu). ListGIF provides a quick analysis solution to identify the overrepresented biomedical concepts from a list of query genes. Result is rendered as a wordle. BUG FIXES o Reactome hyperlink has been fixed. CHANGES IN VERSION 2.0.0 ---------------------- NEW FEATURES o Reactome pathway analysis is based on local reactome.db. The previous xml queries had been disabled. BUG FIXES o Completely support igraph. igraph0 is not supported, which means the nodes index starts at 1, not 0 in igraph0 or less than 0.6.x version igraph. o GO.CC and GO.MF level specified test had been fixed. CHANGES IN VERSION 1.14.0 ---------------------- NEW FEATURES o Multigroup concept-gene analysis html report supports interactive network with cytoscape web support as well as original fixed images o caBIO pathway and REACTOME pathway are included with xml queries, therefore, internet access is required. o The total number of pooled genes in Hypergeometric test can be set by the amount of genes in annotation library or the total annoted genes in the given species. o Add gene annotation summarization functions. Please check geneFunctionSummarize.pdf for more details. CHANGES IN VERSION 1.12.0 ---------------------- NEW FEATURES o Multigroup concept-gene analysis has been added. There are two types of representations. One is graphics table implemented by function 'drawTable', another is a html file generated by function 'groupReport' CHANGES IN VERSION 1.10.0 ---------------------- NEW FEATURES o Shades of nodes are introduced to stand for specified values given in the geneInput slot. o Statistical significant Ontology structure of given terms can be displayed by function 'geneAnswersConceptRelation' so that users can find more appropriate concepts in the significant concept list.