Files in RTCGA/RTCGA
The Cancer Genome Atlas Data Integration
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
ISSUE_TEMPLATE.md
NAMESPACE
NEWS.md
R/RTCGA-package.R
R/boxplotTCGA.R
R/checkTCGA.R
R/convertTCGA.R
R/createTCGA.R
R/datasetsTCGA.R
R/downloadTCGA.R
R/expressionTCGA.R
R/ggbiplot.R
R/heatmapTCGA.R
R/infoTCGA.R
R/installTCGA.R
R/kmTCGA.R
R/mutationsTCGA.R
R/pcaTCGA.R
R/readTCGA.R
R/survivalTCGA.R
R/theme_RTCGA.R
R/zzz.R
README.md
RTCGA.Rproj
RTCGA_workflow.pdf
RTCGA_workflow.png
RTCGA_workflow_ver3.png
UseCases/BigDataInGenomics.pdf
UseCases/MarcinKosinski.pdf
UseCases/backpack.db
UseCases/gallery/07707c687803f7e0893056b2e3c3c985.rda
UseCases/gallery/0a71033d34cb46a62d591537f137cebc.rda
UseCases/gallery/0b676e53342c3f4fabd32bea830f3e38.rda
UseCases/gallery/138dca36b03ff12da14e4089f9caa0d0.rda
UseCases/gallery/33f3a9f48ef8356e4bc80a20b1be3b33.rda
UseCases/gallery/33f3a9f48ef8356e4bc80a20b1be3b33.txt
UseCases/gallery/470516d5f2db4c8fa0dddbe188b09903.rda
UseCases/gallery/49de10580c60b09d1a5c2a65b1df6d93.rda
UseCases/gallery/5cdff52cc239d0a077895d85ef4df5f4.rda
UseCases/gallery/5deb8b80add17d1c6bcadde05953006b.rda
UseCases/gallery/72ce5bca69d4db4beb06e8fad0430dba.rda
UseCases/gallery/79eb5309b4854c9b888f19f943a64bd4.rda
UseCases/gallery/8114f6089aae20d1a37df5b50854b328.rda
UseCases/gallery/a8c532acad91e639c81079e5f5a3a395.rda
UseCases/gallery/ad2ee0eab6c4ebca420d885a0798a4a1.rda
UseCases/gallery/ad2ee0eab6c4ebca420d885a0798a4a1.txt
UseCases/gallery/ba1ad7367d6821b8f7e52c4656a41ff4.rda
UseCases/gallery/c026b0e3f38b1dc62542348ddd9d3c3d.rda
UseCases/gallery/cf5a228b9f27ecea9521e39a2f39796d.rda
UseCases/gallery/d8ca0a226a22d0097c9f9f0ef6d304a0.rda
UseCases/gallery/e05f385c3e0b4009b78427626de1e8f2.rda
UseCases/gallery/ed64b1f42628dd0bbaabb01dcb7b63c7.rda
UseCases/gallery/f9e884084b84794d762a535f3facec85.rda
UseCases/issue1.Rmd
UseCases/issue1.html
UseCases/plakat3_SymbiozaV_04_2016.pdf
_pkgdown.yml
devel/RTCGA.tools/.Rbuildignore
devel/RTCGA.tools/DESCRIPTION
devel/RTCGA.tools/NAMESPACE
devel/RTCGA.tools/R/TP53_variants.R
devel/RTCGA.tools/R/cnv_gene_scores.R
devel/RTCGA.tools/R/mergeTCGA.R
devel/RTCGA.tools/R/misc.R
devel/RTCGA.tools/R/plots.R
devel/RTCGA.tools/RTCGA.tools.Rproj
devel/RTCGA.tools/man/calculate_cooccurence.Rd
devel/RTCGA.tools/man/mergeTCGA.Rd
devel/RTCGA.tools/man/misc.Rd
devel/RTCGA.tools/man/plots.Rd
devel/RTCGA.tools/vignettes/coocurence.Rmd
devel/bioinfo_article/OUP_First_SBk_Bot_8401-eps-converted-to.pdf
devel/bioinfo_article/OUP_First_SBk_Bot_8401.eps
devel/bioinfo_article/Principles_of_Multivariate_Analysis.bibtex
devel/bioinfo_article/Sample.pdf
devel/bioinfo_article/algorithm.sty
devel/bioinfo_article/algorithm2e.sty
devel/bioinfo_article/algorithmic.sty
devel/bioinfo_article/algorithmicx.sty
devel/bioinfo_article/algpseudocode.sty
devel/bioinfo_article/alltt.sty
devel/bioinfo_article/array.sty
devel/bioinfo_article/bibarticle.bib
devel/bioinfo_article/bioinfo.cls
devel/bioinfo_article/caption.sty
devel/bioinfo_article/chngpage.sty
devel/bioinfo_article/color.sty
devel/bioinfo_article/createPlots.R
devel/bioinfo_article/crop.cfg
devel/bioinfo_article/crop.sty
devel/bioinfo_article/document.bib
devel/bioinfo_article/figures/RTCGA.pdf
devel/bioinfo_article/figures/RTCGA_workflow.png
devel/bioinfo_article/figures/RTCGA_workflow_ver3.png
devel/bioinfo_article/figures/RTCGA_workflow_ver4.png
devel/bioinfo_article/figures/boxplot.pdf
devel/bioinfo_article/figures/boxplots.png
devel/bioinfo_article/figures/heatmap.png
devel/bioinfo_article/figures/km.png
devel/bioinfo_article/figures/pca.pdf
devel/bioinfo_article/figures/pca.png
devel/bioinfo_article/figures/rtcga_unified.pdf
devel/bioinfo_article/figures/surv.pdf
devel/bioinfo_article/float.sty
devel/bioinfo_article/flushend.sty
devel/bioinfo_article/graphicx.sty
devel/bioinfo_article/landscap.sty
devel/bioinfo_article/main.bib
devel/bioinfo_article/main.pdf
devel/bioinfo_article/main.tex
devel/bioinfo_article/natbib.bst
devel/bioinfo_article/natbib.sty
devel/bioinfo_article/plain.bst
devel/bioinfo_article/stfloats.sty
devel/bioinfo_article/url.sty
devel/createTCGA.R
devel/createTCGA.Rd
devel/graphs/rnaseq.png
devel/rticle/RJournal.sty
devel/rticle/RJreferences.bib
devel/rticle/RJwrapper.pdf
devel/rticle/RJwrapper.tex
devel/rticle/Rlogo.png
devel/rticle/biplot_rnaseq.pdf
devel/rticle/cnv.pdf
devel/rticle/cnv/downloadCNV.Rmd
devel/rticle/cnv/downloadCNV.html
devel/rticle/download_cnv.Rmd
devel/rticle/km_luad_plot.pdf
devel/rticle/km_plot_luad.pdf
devel/rticle/mutationsBox.pdf
devel/rticle/res_lp_mart.pdf
devel/rticle/rnaseq_biplot.pdf
devel/rticle/rticle.Rmd
devel/rticle/rticle.tex
docs/articles/Data_Download.html
docs/articles/RTCGA_Workflow.R
docs/articles/RTCGA_Workflow.html
docs/articles/RTCGA_Workflow_files/font-awesome-4.5.0/css/font-awesome.css
docs/articles/RTCGA_Workflow_files/font-awesome-4.5.0/css/font-awesome.min.css
docs/articles/RTCGA_Workflow_files/font-awesome-4.5.0/fonts/fontawesome-webfont.ttf
docs/articles/Visualizations.html
docs/articles/Visualizations_files/figure-html/unnamed-chunk-3-1.png
docs/articles/Visualizations_files/figure-html/unnamed-chunk-4-1.png
docs/articles/Visualizations_files/figure-html/unnamed-chunk-5-1.png
docs/articles/Visualizations_files/figure-html/unnamed-chunk-5-2.png
docs/articles/Visualizations_files/figure-html/unnamed-chunk-5-3.png
docs/articles/Visualizations_files/figure-html/unnamed-chunk-6-1.png
docs/articles/Visualizations_files/figure-html/unnamed-chunk-7-1.png
docs/articles/Visualizations_files/figure-html/unnamed-chunk-8-1.png
docs/articles/Visualizations_files/figure-html/unnamed-chunk-9-1.png
docs/articles/Visualizations_files/figure-html/unnamed-chunk-9-2.png
docs/articles/Visualizations_files/figure-html/unnamed-chunk-9-3.png
docs/articles/Web_Applications.html
docs/articles/index.html
docs/authors.html
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/reference/RTCGA-package.html
docs/reference/boxplotTCGA-10.png
docs/reference/boxplotTCGA-12.png
docs/reference/boxplotTCGA-14.png
docs/reference/boxplotTCGA-16.png
docs/reference/boxplotTCGA-18.png
docs/reference/boxplotTCGA-2.png
docs/reference/boxplotTCGA-4.png
docs/reference/boxplotTCGA-6.png
docs/reference/boxplotTCGA-8.png
docs/reference/boxplotTCGA.html
docs/reference/checkTCGA.html
docs/reference/convertTCGA.html
docs/reference/createTCGA.html
docs/reference/datasetsTCGA.html
docs/reference/downloadTCGA.html
docs/reference/expressionsTCGA-12.png
docs/reference/expressionsTCGA-3.png
docs/reference/expressionsTCGA-7.png
docs/reference/expressionsTCGA-9.png
docs/reference/expressionsTCGA.html
docs/reference/heatmapTCGA-2.png
docs/reference/heatmapTCGA-4.png
docs/reference/heatmapTCGA-6.png
docs/reference/heatmapTCGA-8.png
docs/reference/heatmapTCGA.html
docs/reference/index.html
docs/reference/infoTCGA.html
docs/reference/installTCGA.html
docs/reference/kmTCGA-2.png
docs/reference/kmTCGA-4.png
docs/reference/kmTCGA-6.png
docs/reference/kmTCGA.html
docs/reference/mutationsTCGA-2.png
docs/reference/mutationsTCGA.html
docs/reference/pcaTCGA.html
docs/reference/readTCGA.html
docs/reference/survivalTCGA-2.png
docs/reference/survivalTCGA-4.png
docs/reference/survivalTCGA-6.png
docs/reference/survivalTCGA.html
docs/reference/theme_RTCGA-2.png
docs/reference/theme_RTCGA.html
inst/createTCGA.Rmd
man-roxygen/roxlate-ggtheme.R
man/RTCGA-package.Rd
man/boxplotTCGA.Rd
man/checkTCGA.Rd
man/convertTCGA.Rd
man/createTCGA.Rd
man/datasetsTCGA.Rd
man/downloadTCGA.Rd
man/expressionsTCGA.Rd
man/heatmapTCGA.Rd
man/infoTCGA.Rd
man/installTCGA.Rd
man/kmTCGA.Rd
man/mutationsTCGA.Rd
man/pcaTCGA.Rd
man/readTCGA.Rd
man/survivalTCGA.Rd
man/theme_RTCGA.Rd
tests/testthat.R
tests/testthat/test_check.R
tests/testthat/test_convert.R
tests/testthat/test_download.R
tests/testthat/test_info.R
tests/testthat/test_read.R
update_remotes.sh
vignettes/Data_Download.Rmd
vignettes/RTCGA_Workflow.Rmd
vignettes/Visualizations.Rmd
