CHANGES IN VERSION 1.2.21 (17 February 2017) ------------------------ Last commit was not completed CHANGES IN VERSION 1.0.16 (03 January 2017) ------------------------ o update documents CHANGES IN VERSION 1.0.13 (28 December 2016) ------------------------ o Reactome tab update CHANGES IN VERSION 1.0.12 (27 December 2016) ------------------------ o Simplify genes classification CHANGES IN VERSION 1.0.10 (25 December 2016) ------------------------ o clarify interface: Pipeline Overview o remove Cluster and Factor Menus CHANGES IN VERSION 1.0.07 (14 December 2016) ------------------------ o add argument to whichGeneLits(input$GeneListID) o Use the SUM of mutation cases and NOT SUM/TOTAL_SUM (ratio) o replace dplyr::add_rownames() by tibble::rownames_to_column() o replace stopping process (stop function) by warning message. stop function disconnect session in server version. o resolve error message when Gene list is empty (paste empty gene list). getListProfData, getFreqMutData, ProfData, MutData, Classifier, geNetClassifier, Circomics_ui, getCircomics, Reactome_ui. o Make it possible to get Circomics only for one study. Essentially resolve data structure in processing of mutation data frame. CHANGES IN VERSION 1.0.03 (29 Septembre 2016) ------------------------ o update pivotr from radiant.data CHANGES IN VERSION 1.0.02 (29 Septembre 2016) ------------------------ o replace dplyr::add_rownames() by tibble::rownames_to_column() CHANGES IN VERSION 1.0.01 (29 Septembre 2016) ------------------------ o rm "id=" from navbarMenu - shiny update CHANGES IN VERSION 1.0.0 (07 July 2016) ------------------------ o built vignette with knitr o modify whichGeneList(GeneListLabel) resolve difference between bioCancer server and package FIRST RELEASE o Package released o Omit R/code menu: request shinyAce (>=0.2.1) - Omit help_and_report function o Various issues request DT (>=0.1.39) - Omit Show Plot in Pivot sidebar menu - Can not download/Store correctly filtered table in Handle/View PERSPECTIVE o Release R 3.4 import(shiny, except= c("dataTableOutput", "renderDataTable")) o use DisGeNet server despite /extdata/disGeNet file (DONE Not Working) o clusterProfiler GMT file: http://www.r-bloggers.com/go-analysis-using-clusterprofiler/ o gene classification using rpart,ggplot2, ggtree: http://guangchuangyu.github.io/2016/01/annotate-a-phylogenetic-tree-with-insets/ o Specify the range of mutation frequency in circos plot [Min, Max]