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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 (3.19)

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 "4.4") 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 2.3.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports utils, data.table, plyr, cqn, topconfects, stats, SummarizedExperiment, methods
System Requirements
URL https://github.com/YuLab-SMU/GeoTcgaData
Bug Reports https://github.com/YuLab-SMU/GeoTcgaData/issues
See More
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
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Package Archives

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

Source Package GeoTcgaData_2.3.0.tar.gz
Windows Binary GeoTcgaData_2.3.0.zip
macOS Binary (x86_64) GeoTcgaData_2.3.0.tgz
macOS Binary (arm64) GeoTcgaData_2.3.0.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