---
title: "RTCGA package workflow"
subtitle: "[rtcga.github.io/RTCGA/](https://rtcga.github.io/RTCGA/)"
author: "Marcin Kosinski&nbsp;&nbsp;<small><a href='http://r-addict.com'><i class='fa fa-comment'></i></a>&nbsp;&nbsp;<a href='https://stackoverflow.com/users/3857701'><i class='fa fa-stack-overflow'></i></a>&nbsp;&nbsp;<a href='https://github.com/MarcinKosinski'><i class='fa fa-github'></i></a>&nbsp;&nbsp;<a href='mailto:m.p.kosinski@gmail.com'><i class='fa fa-envelope-o'></i></a></small><br>"
date: "2016-12-09"
output:
  html_document:
    theme: readable
    highlight: tango
    fig_width: 17
    fig_height: 10
    toc: false
vignette: >
  %\VignetteIndexEntry{Integrating TCGA Data - RTCGA Workflow}
  %\VignetteEngine{knitr::rmarkdown}
---

```{r, include=FALSE}
htmltools::tagList(rmarkdown::html_dependency_font_awesome())
library(knitr)
opts_chunk$set(
	comment = "",
	fig.width = 12, 
	message = FALSE,
	warning = FALSE,
	tidy.opts = list(
		keep.blank.line = TRUE,	
		width.cutoff = 150
		),
	options(width = 200),
	eval = TRUE
)
```


<img src="https://raw.githubusercontent.com/RTCGA/RTCGA/master/RTCGA_workflow.png" height="500" width="800">

Data packages **not yet** submitted to Bioconductor from 2016-01-28 release date of TCGA data.

- [RTCGA.mutations.20160128](http://github.com/RTCGA/RTCGA.mutations.20160128/)
- [RTCGA.rnaseq.20160128](http://github.com/RTCGA/RTCGA.rnaseq.20160128/)
- [RTCGA.clinical.20160128](http://github.com/RTCGA/RTCGA.clinical.20160128/)
- [RTCGA.mRNA.20160128](http://github.com/RTCGA/RTCGA.mRNA.20160128/)
- [RTCGA.miRNASeq.20160128](http://github.com/RTCGA/RTCGA.miRNASeq.20160128/)
- [RTCGA.RPPA.20160128](http://github.com/RTCGA/RTCGA.RPPA.20160128/)
- [RTCGA.CNV.20160128](http://github.com/RTCGA/RTCGA.CNV.20160128/)
- [RTCGA.methylation.20160128](http://github.com/RTCGA/RTCGA.methylation.20160128/)



Data packages submitted to Bioconductor from 2015-11-01 release date of TCGA data.

- [RTCGA.mutations](http://bioconductor.org/packages/RTCGA.mutations/)
- [RTCGA.rnaseq](http://bioconductor.org/packages/RTCGA.rnaseq/)
- [RTCGA.clinical](http://bioconductor.org/packages/RTCGA.clinical/)
- [RTCGA.PANCAN12](http://bioconductor.org/packages/RTCGA.PANCAN12/)
- [RTCGA.mRNA](http://bioconductor.org/packages/RTCGA.mRNA/)
- [RTCGA.miRNASeq](http://bioconductor.org/packages/RTCGA.miRNASeq/)
- [RTCGA.RPPA](http://bioconductor.org/packages/RTCGA.RPPA/)
- [RTCGA.CNV](http://bioconductor.org/packages/RTCGA.CNV/)
- [RTCGA.methylation](http://bioconductor.org/packages/RTCGA.methylation/)