#' @title TCGAWorkflow
#' @description
#' Biotechnological advances in sequencing have led to an explosion of
#' publicly available data via large international consortia such as
#' the NCI Genomic Data Commons (GDC), The
#' Encyclopedia of DNA Elements (ENCODE),
#' and The NIH Roadmap Epigenomics Mapping Consortium
#' (Roadmap). These projects have provided unprecedented opportunities to interrogate the epigenome of
#' cultured cancer cell lines as well as normal and tumor tissues with high
#' genomic resolution. The Bioconductor project offers more than 1,000 open-source software and statistical
#' packages to analyze high-throughput genomic data. However, most packages
#' are designed for specific data types (e.g. expression, epigenetics,
#' genomics) and there is no one comprehensive tool that provides a
#' complete integrative analysis of the resources and data provided by all
#' three public projects. A need to create an integration of these
#' different analyses was recently proposed. In this workflow, we provide a
#' series of biologically focused integrative analyses of different
#' molecular data. We describe how to download, process and prepare TCGA
#' data and by harnessing several key Bioconductor packages, we describe
#' how to extract biologically meaningful genomic and epigenomic data.
#' Using Roadmap and ENCODE data, we provide a work plan to identify
#' biologically relevant functional epigenomic elements associated with
#' cancer.
#' To illustrate our workflow, we analyzed two types of brain tumors:
#' low-grade glioma (LGG) versus high-grade glioma (glioblastoma multiform or GBM).
#' @docType package
#' @name TCGAWorkflow
#' @import ELMER downloader SummarizedExperiment TCGAWorkflowData knitr
#' @import ChIPseeker ComplexHeatmap maftools
#' @import minet c3net biomaRt pathview
#' @import motifStack TCGAbiolinks graphics pander
#' @import circlize pbapply GenomeInfoDb ggplot2 ggthemes parallel
#' @importFrom rGADEM GADEM nOccurrences getPWM consensus nMotifs
#' @importFrom AnnotationHub query AnnotationHub
#' @importFrom clusterProfiler bitr
#' @import gt DT BSgenome.Hsapiens.UCSC.hg19 GenomicRanges RTCGAToolbox ggpubr
NULL
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.