GeoTcgaData

Processing Various Types of Data on GEO and TCGA

Bioconductor version: Release (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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ATACSeq, CopyNumberVariation, DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, MethylationArray, Microarray, RNASeq, SNP, Software
Version	2.4.0
In Bioconductor since	BioC 3.17 (R-4.3) (1.5 years)
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

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
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	GeoTcgaData_2.4.0.tar.gz
Windows Binary (x86_64)	GeoTcgaData_2.4.0.zip
macOS Binary (x86_64)	GeoTcgaData_2.4.0.tgz
macOS Binary (arm64)	GeoTcgaData_2.4.0.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