This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

GeoTcgaData

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

Processing Various Types of Data on GEO and TCGA

Bioconductor version: Development (3.18)

Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.

Author: Erqiang Hu [aut, cre]

Maintainer: Erqiang Hu <13766876214 at 163.com>

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("GeoTcgaData")

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("GeoTcgaData")
GeoTcgaData HTML R Script
Reference Manual PDF

Details

biocViews ATACSeq, CopyNumberVariation, DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, MethylationArray, Microarray, RNASeq, SNP, Software
Version 2.1.0
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports utils, data.table, plyr, cqn, topconfects, stats, SummarizedExperiment, methods
Linking To
Suggests knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr, clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq, testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery, BiocGenerics
System Requirements
Enhances
URL https://github.com/YuLab-SMU/GeoTcgaData
Bug Reports https://github.com/YuLab-SMU/GeoTcgaData/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package GeoTcgaData_2.1.0.tar.gz
Windows Binary GeoTcgaData_2.1.0.zip
macOS Binary (x86_64) GeoTcgaData_2.1.0.tgz
macOS Binary (arm64) GeoTcgaData_2.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GeoTcgaData
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GeoTcgaData
Bioc Package Browser https://code.bioconductor.org/browse/GeoTcgaData/
Package Short Url https://bioconductor.org/packages/GeoTcgaData/
Package Downloads Report Download Stats