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Bioconductor - GeoTcgaData (development version)

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 (3.22)

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: 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")

# 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")
Details biocViews ATACSeq, CopyNumberVariation, DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, MethylationArray, Microarray, RNASeq, SNP, Software Version 2.9.0 In Bioconductor since BioC 3.17 (R-4.3) (2 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 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 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.

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