CHANGES IN VERSION 1.30.07 (14 February 2024) -------------------------------------------- + fix issues in Networking Tab CHANGES IN VERSION 1.30.06 (11 February 2024) -------------------------------------------- + Merge mutation and Genetic Ptofile tabs CHANGES IN VERSION 1.30.05 (09 February 2024) -------------------------------------------- + rewrite the function getListProfData + Omit function getMegaProfData user for genlist upper that 500. CHANGES IN VERSION 1.30.04 (05 February 2024) -------------------------------------------- + update ReactomeFI2021.RDS + update DisGeNet0223.RDS CHANGES IN VERSION 1.30.03 (03 February 2024) -------------------------------------------- + update documentatio with new webapi + progress in migration CHANGES IN VERSION 1.30.02 (02 February 2024) -------------------------------------------- + Start migration of cBioportal tab with the new cBioPortal webAPI CHANGES IN VERSION 1.30.01 (20 January 2024) -------------------------------------------- + Update api link CHANGES IN VERSION 1.29.05 (19 October 2023) -------------------------------------------- + Comment pickGO during running examples: It works manually. CHANGES IN VERSION 1.29.01 (28 September 2023) -------------------------------------------- + Correct items format in NEWS file + Import needed packages + Add @method section in documentation of cgdsr methods + Update links and reference in the vignette CHANGES IN VERSION 1.23.03 (25 April 2022) -------------------------------------------- + host cgdsr CHANGES IN VERSION 1.23.02 (19 April 2022) -------------------------------------------- + Update NEWS CHANGES IN VERSION 1.23.01 (14 April 2022) -------------------------------------------- + get cgdsr from github CHANGES IN VERSION 1.15.03 (18 March 2020) ------------------------ + Downgrade DiagrammeR from 1.05 to 1.01. Unable to run a Shiny App using grVizOutput() and renderGrViz() CHANGES IN VERSION 1.15.02 (17 March 2020) ------------------------ + update help page + rename www/imgs to www/logo: confict with www/imgs of rediant.data package. CHANGES IN VERSION 1.15.01 (16 March 2020) ------------------------ + Change the address of reactomeFI from "http://reactomews.oicr.on.ca:8080/" to "http://cpws.reactome.org/" + update ReactomeFI2018.RDS CHANGES IN VERSION 1.11.00 (12 February 2019) ------------------------ + Change the address of cgdsr: http://www.cbioportal.org/ instead http://www.cbioportal.org/public-portal/ CHANGES IN VERSION 1.9.07 (04 September 2018) ------------------------ + replace DOSE::dotplot by clusterProfiler::dotplot + replace r_data by r_info in reports + not need to define genelist in r_data + update ReactomeFI.RDS file (version 2017) + update DisGeNet0918.RDS file (version September 2018), move it from wiki.ubuntu.com to github/kmezhoud CHANGES IN VERSION 1.9.06 (30 August 2018) ------------------------ + rm warning message for min and max functions + run getFreqMutData() when getListProfData() instead getCoffeeWheel_Mut(). Avoid error when loading x profiles data to workspace. + include Tools panel into Workspace panel. + update Overview image CHANGES IN VERSION 1.9.05 (25 August 2018) ------------------------ + r_data vs r_info ... https://radiant-rstats.github.io/docs/news.html + use r_info for dataset list and r_data for genes list + set progress bar CHANGES IN VERSION 1.9.04 (22 August 2018) ------------------------ + add style.css file: reduce padding-top to 0px CHANGES IN VERSION 1.9.03 (16 August 2018) ------------------------ + modify stop function + update paste gene list function CHANGES IN VERSION 1.9.02 (16 August 2018) ------------------------ + upload and download using Rstudio file browser remove plot_downloader function and replace it by download_link (defined in radiant.R file) + add radiant_old.R file for needed functions but not longer used by radiant.data CHANGES IN VERSION 1.9.01 (12 August 2018) ------------------------ + replace getdata() by get_data() + replace factorizer() by lapply(.,factor) CHANGES IN VERSION 1.7.05 (12 April 2018) ------------------------ + omit importFrom clusterProfiler plot CHANGES IN VERSION 1.7.04 (20 November 2017) ------------------------ + export Diagrammer and viNetwork to report + reset image size of circomics to 1024px CHANGES IN VERSION 1.7.03 (20 November 2017) ------------------------ + Save network widgets as HTML and png + use swithc buttom for Networking Tab. + setwd(~)/ for windows system by setwd(Sys.getenv("R_USER")) CHANGES IN VERSION 1.7.02 (14 November 2017) ------------------------ + resolve conflicts renderMetabologram and renderCoffeewheel. redefine initCoffeewhell in /htmlwidges + report circomics widget to markdown document + Save static wheel as html and png (low resolution) + need phantomJS to catupe html widget output as png file CHANGES IN VERSION 1.7.01 (13 November 2017) ------------------------ + add helps to ? menu + change stop message + addResourcePath for figures CHANGES IN VERSION 1.7.00 (30 October 2017) ------------------------ + metamorphosis: bioCancer is a radiant.data extension + reduce size of package by half 14 -> 7 mb CHANGES IN VERSION 1.5.12 (16 October 2017) ------------------------ + improve Reactome_ui functions CHANGES IN VERSION 1.5.11 (16 October 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) ------------------------ + update documents CHANGES IN VERSION 1.0.13 (28 December 2016) ------------------------ + Reactome tab update CHANGES IN VERSION 1.0.12 (27 December 2016) ------------------------ + Simplify genes classification CHANGES IN VERSION 1.0.10 (25 December 2016) ------------------------ + clarify interface: Pipeline Overview + remove Cluster and Factor Menus CHANGES IN VERSION 1.0.07 (14 December 2016) ------------------------ + add argument to whichGeneLits(input$GeneListID) + Use the SUM of mutation cases and NOT SUM/TOTAL_SUM (ratio) + replace dplyr::add_rownames() by tibble::rownames_to_column() + replace stopping process (stop function) by warning message. stop function disconnect session in server version. + resolve error message when Gene list is empty (paste empty gene list). getListProfData, getFreqMutData, ProfData, MutData, Classifier, geNetClassifier, Circomics_ui, getCircomics, Reactome_ui. + 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) ------------------------ + update pivotr from radiant.data CHANGES IN VERSION 1.0.02 (29 Septembre 2016) ------------------------ + replace dplyr::add_rownames() by tibble::rownames_to_column() CHANGES IN VERSION 1.0.01 (29 Septembre 2016) ------------------------ + rm "id=" from navbarMenu - shiny update CHANGES IN VERSION 1.0.0 (07 July 2016) ------------------------ + built vignette with knitr + modify whichGeneList(GeneListLabel) resolve difference between bioCancer server and package FIRST RELEASE + Package released + Omit R/code menu: request shinyAce (>=0.2.1) - Omit help_and_report function + 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 + Check add interesting genes in networking Tab + 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)" + use DisGeNet server despite /extdata/disGeNet file (DONE Not Working) + clusterProfiler GMT file: - http://www.r-bloggers.com/go-analysis-using-clusterprofiler/ + gene classification using rpart,ggplot2, ggtree: - http://guangchuangyu.github.io/2016/01/annotate-a-phylogenetic-tree-with-insets/ + Specify the range of mutation frequency in circos plot [Min, Max]