HarmonizedTCGAData
This is the development version of HarmonizedTCGAData; for the stable release version, see HarmonizedTCGAData.
Processed Harmonized TCGA Data of Five Selected Cancer Types
Bioconductor version: Development (3.24)
This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering".
Author: Tianle Ma
Maintainer: Tianle Ma <tianlema at buffalo.edu>
citation("HarmonizedTCGAData")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("HarmonizedTCGAData")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HarmonizedTCGAData")| Patient Affinity Matrices Derived from Harmonized TCGA Dataset | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CancerData, ExperimentData, ReproducibleResearch |
| Version | 1.35.0 |
| License | GPL-3 |
| Depends | R (>= 3.4.0) |
| Imports | ExperimentHub |
| System Requirements | |
| URL |
See More
| Suggests | AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HarmonizedTCGAData_1.35.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/HarmonizedTCGAData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HarmonizedTCGAData |
| Package Short Url | https://bioconductor.org/packages/HarmonizedTCGAData/ |
| Package Downloads Report | Download Stats |