NEWS
bioCancer 1.30.07
- fix issues in Networking Tab
bioCancer 1.30.06
- Merge mutation and Genetic Ptofile tabs
bioCancer 1.30.05
- rewrite the function getListProfData
- Omit function getMegaProfData user for genlist upper that 500.
bioCancer 1.30.04
- update ReactomeFI2021.RDS
- update DisGeNet0223.RDS
bioCancer 1.30.03
- update documentatio with new webapi
- progress in migration
bioCancer 1.30.02
- Start migration of cBioportal tab with the new cBioPortal webAPI
bioCancer 1.30.01
bioCancer 1.29.05
- Comment pickGO during running examples: It works manually.
bioCancer 1.29.01
- Correct items format in NEWS file
- Import needed packages
- Add @method section in documentation of cgdsr methods
- Update links and reference in the vignette
bioCancer 1.23.03
bioCancer 1.23.02
bioCancer 1.23.01
bioCancer 1.15.03
- Downgrade DiagrammeR from 1.05 to 1.01. Unable to run a Shiny App using grVizOutput() and renderGrViz()
bioCancer 1.15.02
- update help page
- rename www/imgs to www/logo: confict with www/imgs of rediant.data package.
bioCancer 1.15.01
- Change the address of reactomeFI from "http://reactomews.oicr.on.ca:8080/" to "http://cpws.reactome.org/"
- update ReactomeFI2018.RDS
bioCancer 1.11.00
- Change the address of cgdsr: http://www.cbioportal.org/ instead http://www.cbioportal.org/public-portal/
bioCancer 1.9.07
- 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
bioCancer 1.9.06
- 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
bioCancer 1.9.05
- 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
bioCancer 1.9.04
- add style.css file: reduce padding-top to 0px
bioCancer 1.9.03
- modify stop function
- update paste gene list function
bioCancer 1.9.02
- 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
bioCancer 1.9.01
- replace getdata() by get_data()
- replace factorizer() by lapply(.,factor)
bioCancer 1.7.05
- omit importFrom clusterProfiler plot
bioCancer 1.7.04
- export Diagrammer and viNetwork to report
- reset image size of circomics to 1024px
bioCancer 1.7.03
- Save network widgets as HTML and png
- use swithc buttom for Networking Tab.
- setwd(~)/ for windows system by setwd(Sys.getenv("R_USER"))
bioCancer 1.7.02
- 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
bioCancer 1.7.01
- add helps to ? menu
- change stop message
- addResourcePath for figures
bioCancer 1.7.00
- metamorphosis: bioCancer is a radiant.data extension
- reduce size of package by half 14 -> 7 mb
bioCancer 1.5.12
- improve Reactome_ui functions
bioCancer 1.5.11
- add switch button to ui_circomics
- improve circomics functions
bioCancer 1.5.09
- delete commented files and figures
- cleanup ui_radiant, /Rbis, /quant, /bioCancer
bioCancer 1.5.08
bioCancer 1.5.07
- data.row.names(row.names, rowsi, i) :
- some row.names duplicated: 11,12,13,14 --> row.names NOT used
bioCancer 1.5.06
- dplyr::mutate_each() is deprecated
- dply::summarise_each() is deprecated
replace BiocStyle by prettydoc
bioCancer 1.5.05
- Warning in formals(fun) : argument is not a function
- Warning in body(fun) : argument is not a function
bioCancer 1.5.04
bioCancer 1.5.03
- Change the color rang of Circular layout plot as in standards
bioCancer 1.5.02
- update Correlation Methods
bioCancer 1.5.01
- replace .libPath() by path.package('bioCancer') in portal.R file
bioCancer 1.0.16
bioCancer 1.0.13
bioCancer 1.0.12
- Simplify genes classification
bioCancer 1.0.10
- clarify interface: Pipeline Overview
- remove Cluster and Factor Menus
bioCancer 1.0.07
- 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.
bioCancer 1.0.03
- update pivotr from radiant.data
bioCancer 1.0.02
- replace dplyr::add_rownames() by tibble::rownames_to_column()
bioCancer 1.0.01
- rm "id=" from navbarMenu - shiny update
bioCancer 1.0.0
- 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]