CHANGES IN VERSION 1.6.00 (30 November 2017) ------------------------ metamorphosis: bioCancer is a radiant.data extension reduce size of package by half 14 -> 7 mb CHANGES IN VERSION 1.5.12 (16 November 2017) ------------------------ improve Reactome_ui functions CHANGES IN VERSION 1.5.11 (16 November 2017) ------------------------ add switch button to ui_circomics improve circomics functions CHANGES IN VERSION 1.5.09 (08 September 2017) ------------------------ delete commented files and figures CHANGES IN VERSION 1.5.09 (07 September 2017) ------------------------ cleanup ui_radiant, /Rbis, /quant, /bioCancer CHANGES IN VERSION 1.5.08 (1 September 2017) ------------------------ switchButton CHANGES IN VERSION 1.5.07 (1 September 2017) ------------------------ data.row.names(row.names, rowsi, i) : some row.names duplicated: 11,12,13,14 --> row.names NOT used CHANGES IN VERSION 1.5.06 (1 September 2017) ------------------------ dplyr::mutate_each() is deprecated dply::summarise_each() is deprecated replace BiocStyle by prettydoc CHANGES IN VERSION 1.5.05 (1 September 2017) ------------------------ Warning in formals(fun) : argument is not a function Warning in body(fun) : argument is not a function CHANGES IN VERSION 1.5.04 (02 July 2017) ------------------------ Fix setting plot size CHANGES IN VERSION 1.5.03 (31 May 2017) ------------------------ Change the color rang of Circular layout plot as in standards CHANGES IN VERSION 1.5.02 (30 May 2017) ------------------------ update Correlation Methods CHANGES IN VERSION 1.5.01 (29 May 2017) ------------------------ replace .libPath() by path.package('bioCancer') in portal.R file 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]