GeoTcgaData
This is the released version of GeoTcgaData; for the devel version, see GeoTcgaData.
Processing Various Types of Data on GEO and TCGA
Bioconductor version: Release (3.23)
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.
Maintainer: Erqiang Hu <13766876214 at 163.com>
citation("GeoTcgaData")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 |
Details
| biocViews | ATACSeq, CopyNumberVariation, DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, MethylationArray, Microarray, RNASeq, SNP, Software |
| Version | 2.12.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 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 |
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.
| Source Package | GeoTcgaData_2.12.0.tar.gz |
| Windows Binary (x86_64) | GeoTcgaData_2.12.0.zip |
| macOS Binary (big-sur-x86_64) | GeoTcgaData_2.12.0.tgz |
| macOS Binary (sonoma-arm64) | GeoTcgaData_2.12.0.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 |