GeoTcgaData
Processing Various Types of Data on GEO and TCGA
Bioconductor version: 3.23 · Package version: 2.12.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GeoTcgaData")Details
| Maintainer | Erqiang Hu <13766876214@163.com> |
| Author | Erqiang Hu [aut, cre] (ORCID: <https://orcid.org/0000-0002-1798-7513>) |
| License | Artistic-2.0 |
| URL | https://github.com/YuLab-SMU/GeoTcgaData |
| Bug Reports | https://github.com/YuLab-SMU/GeoTcgaData/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ATACSeq, CopyNumberVariation, DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, MethylationArray, Microarray, RNASeq, SNP, Software |
| Package Short Url | https://bioconductor.org/packages/GeoTcgaData/ |
Citation
From within R, enter citation("GeoTcgaData"):
Erqiang Hu. GeoTcgaData: Processing Various Types of Data on GEO and TCGA. doi:10.18129/B9.bioc.GeoTcgaData, R package version 2.12.0, https://bioconductor.org/packages/GeoTcgaData.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | GeoTcgaData_2.12.0.tar.gz |
| Windows binary (x86_64) | GeoTcgaData_2.12.0.zip |
| macOS binary (arm64) | GeoTcgaData_2.12.0.tgz |
| macOS binary (x86_64) | GeoTcgaData_2.12.0.tgz |
Dependencies
Depends: R (>= 4.2.0)
Imports: utils, data.table, plyr, cqn, topconfects, stats, SummarizedExperiment, methods
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