TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
Bioconductor version: 3.23 · Package version: 2.40.0
The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TCGAbiolinks")Details
| Maintainer | Tiago Chedraoui Silva <tiagochst@gmail.com>, Antonio Colaprico <axc1833@med.miami.edu> |
| Author | Antonio Colaprico, Tiago Chedraoui Silva, Catharina Olsen, Luciano Garofano, Davide Garolini, Claudia Cava, Thais Sabedot, Tathiane Malta, Stefano M. Pagnotta, Isabella Castiglioni, Michele Ceccarelli, Gianluca Bontempi, Houtan Noushmehr |
| License | GPL (>= 3) |
| URL | https://github.com/BioinformaticsFMRP/TCGAbiolinks |
| Bug Reports | https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues |
| Downloads rank | 6244 |
| Source branch | RELEASE_3_23 |
| biocViews | DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Sequencing, Software, Survival |
Documentation
- Introduction
- TCGAbiolinks version bump with new functions
- TCGAbiolinks: Searching GDC database
- TCGAbiolinks: Downloading and preparing files for analysis
- TCGAbiolinks: Clinical data
- TCGAbiolinks: Searching, downloading and visualizing mutation files
- Classifiers methods
- Stemness score
- Compilation of TCGA molecular subtypes
- Analyzing and visualizing TCGA data
- Case Studies
Download
Dependencies
Depends: R (>= 4.1.0)
Imports: downloader (>= 0.4), grDevices, biomaRt, dplyr, graphics, tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite (>= 1.0.0), plyr, knitr, methods, ggplot2, stringr (>= 1.0.0), IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils, SummarizedExperiment (>= 1.4.0), TCGAbiolinksGUI.data (>= 1.15.1), readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1)
Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, Biobase, affy, testthat, sesame, AnnotationHub, ExperimentHub, pathview, clusterProfiler, Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid, DT
Reverse dependencies
Imports Me (6): CBN2Path, ELMER, miRLAB, MoonlightR, SurfR, TENET
Suggests Me (4): GeoTcgaData, iNETgrate, musicatk, oncoPredict