Changes in version 1.30.07 o fix issues in Networking Tab Changes in version 1.30.06 o Merge mutation and Genetic Ptofile tabs Changes in version 1.30.05 o rewrite the function getListProfData o Omit function getMegaProfData user for genlist upper that 500. Changes in version 1.30.04 o update ReactomeFI2021.RDS o update DisGeNet0223.RDS Changes in version 1.30.03 o update documentatio with new webapi o progress in migration Changes in version 1.30.02 o Start migration of cBioportal tab with the new cBioPortal webAPI Changes in version 1.30.01 o Update api link Changes in version 1.29.05 o Comment pickGO during running examples: It works manually. Changes in version 1.29.01 o Correct items format in NEWS file o Import needed packages o Add @method section in documentation of cgdsr methods o Update links and reference in the vignette Changes in version 1.23.03 o host cgdsr Changes in version 1.23.02 o Update NEWS Changes in version 1.23.01 o get cgdsr from github Changes in version 1.15.03 o Downgrade DiagrammeR from 1.05 to 1.01. Unable to run a Shiny App using grVizOutput() and renderGrViz() Changes in version 1.15.02 o update help page o rename www/imgs to www/logo: confict with www/imgs of rediant.data package. Changes in version 1.15.01 o Change the address of reactomeFI from "http://reactomews.oicr.on.ca:8080/" to "http://cpws.reactome.org/" o update ReactomeFI2018.RDS Changes in version 1.11.00 o Change the address of cgdsr: http://www.cbioportal.org/ instead http://www.cbioportal.org/public-portal/ Changes in version 1.9.07 o replace DOSE::dotplot by clusterProfiler::dotplot o replace r_data by r_info in reports o not need to define genelist in r_data o update ReactomeFI.RDS file (version 2017) o update DisGeNet0918.RDS file (version September 2018), move it from wiki.ubuntu.com to github/kmezhoud Changes in version 1.9.06 o rm warning message for min and max functions o run getFreqMutData() when getListProfData() instead getCoffeeWheel_Mut(). Avoid error when loading x profiles data to workspace. o include Tools panel into Workspace panel. o update Overview image Changes in version 1.9.05 o r_data vs r_info ... https://radiant-rstats.github.io/docs/news.html o use r_info for dataset list and r_data for genes list o set progress bar Changes in version 1.9.04 o add style.css file: reduce padding-top to 0px Changes in version 1.9.03 o modify stop function o update paste gene list function Changes in version 1.9.02 o upload and download using Rstudio file browser remove plot_downloader function and replace it by download_link (defined in radiant.R file) o add radiant_old.R file for needed functions but not longer used by radiant.data Changes in version 1.9.01 o replace getdata() by get_data() o replace factorizer() by lapply(.,factor) Changes in version 1.7.05 o omit importFrom clusterProfiler plot Changes in version 1.7.04 o export Diagrammer and viNetwork to report o reset image size of circomics to 1024px Changes in version 1.7.03 o Save network widgets as HTML and png o use swithc buttom for Networking Tab. o setwd(~)/ for windows system by setwd(Sys.getenv("R_USER")) Changes in version 1.7.02 o resolve conflicts renderMetabologram and renderCoffeewheel. redefine initCoffeewhell in /htmlwidges o report circomics widget to markdown document o Save static wheel as html and png (low resolution) o need phantomJS to catupe html widget output as png file Changes in version 1.7.01 o add helps to ? menu o change stop message o addResourcePath for figures Changes in version 1.7.00 o metamorphosis: bioCancer is a radiant.data extension o reduce size of package by half 14 -> 7 mb Changes in version 1.5.12 o improve Reactome_ui functions Changes in version 1.5.11 o add switch button to ui_circomics o improve circomics functions Changes in version 1.5.09 o delete commented files and figures o cleanup ui_radiant, /Rbis, /quant, /bioCancer Changes in version 1.5.08 o switchButton Changes in version 1.5.07 o data.row.names(row.names, rowsi, i) : o some row.names duplicated: 11,12,13,14 --> row.names NOT used Changes in version 1.5.06 o dplyr::mutate_each() is deprecated o dply::summarise_each() is deprecated replace BiocStyle by prettydoc Changes in version 1.5.05 o Warning in formals(fun) : argument is not a function o Warning in body(fun) : argument is not a function Changes in version 1.5.04 o Fix setting plot size Changes in version 1.5.03 o Change the color rang of Circular layout plot as in standards Changes in version 1.5.02 o update Correlation Methods Changes in version 1.5.01 o replace .libPath() by path.package('bioCancer') in portal.R file Changes in version 1.0.16 o update documents Changes in version 1.0.13 o Reactome tab update Changes in version 1.0.12 o Simplify genes classification Changes in version 1.0.10 o clarify interface: Pipeline Overview o remove Cluster and Factor Menus Changes in version 1.0.07 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 o update pivotr from radiant.data Changes in version 1.0.02 o replace dplyr::add_rownames() by tibble::rownames_to_column() Changes in version 1.0.01 o rm "id=" from navbarMenu - shiny update Changes in version 1.0.0 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 Check add interesting genes in networking Tab o Visualize all cases and genetic profiles for studies - Visualize samples SIZE for each cases/genetic profile - for gbm_tcga there are 3 samples size for mRNA expression: o "Samples with mRNA expression data (166 samples)" o "Samples with mRNA expression data (401 samples)" o Samples with mRNA expression data (528 samples)" 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]