GSE62944

This is the development version of GSE62944; for the stable release version, see GSE62944.

GEO accession data GSE62944 as a SummarizedExperiment

Bioconductor version: Development (3.24)

TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub.

Author: Sonali Arora

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("GSE62944")):

Seminal Bioconductor project articles:

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("GSE62944")

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("GSE62944")

Raw TCGA data using Bioconductor's ExperimentHub	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNASeqData, ExperimentData, Genome, RNASeqData
Version	1.41.0
License	Artistic-2.0
Depends	Biobase, GEOquery
Imports
System Requirements
URL	http://bioconductor.org/packages/release/bioc/html/GSE62944.html

Suggests	ExperimentHub(>= 0.99.6), knitr, BiocStyle, rmarkdown, DESeq2
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	GSEABenchmarkeR
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GSE62944_1.41.0.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/GSE62944
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GSE62944
Package Short Url	https://bioconductor.org/packages/GSE62944/
Package Downloads Report	Download Stats