GeoTcgaData

DOI: 10.18129/B9.bioc.GeoTcgaData  

Processing Various Types of Data on GEO and TCGA

Bioconductor version: Release (3.17)

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>

Installation

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

 

HTML	R Script	GeoTcgaData
PDF		Reference Manual

Details

biocViews	ATACSeq, CopyNumberVariation, DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, MethylationArray, Microarray, RNASeq, SNP, Software
Version	2.0.0
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
LinkingTo
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
SystemRequirements
Enhances
URL	https://github.com/YuLab-SMU/GeoTcgaData
BugReports	https://github.com/YuLab-SMU/GeoTcgaData/issues
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_2.0.0.tar.gz
Windows Binary	GeoTcgaData_2.0.0.zip
macOS Binary (x86_64)	GeoTcgaData_2.0.0.tgz
macOS Binary (arm64)	GeoTcgaData_2.0.0.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
Old Source Packages for BioC 3.17	Source Archive