GeoTcgaData

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see GeoTcgaData.

Processing Various Types of Data on GEO and TCGA

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0002-1798-7513

Maintainer: Erqiang Hu <13766876214 at 163.com>

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

Installation

To install this package, start R (version "4.5") 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 2.8.0

In Bioconductor since BioC 3.17 (R-4.3) (2.5 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

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Package Archives

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

Source Package GeoTcgaData_2.8.0.tar.gz

Windows Binary (x86_64) GeoTcgaData_2.8.0.zip

macOS Binary (x86_64) GeoTcgaData_2.8.0.tgz

macOS Binary (arm64) GeoTcgaData_2.8.0.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/

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