GeoTcgaData
Processing Various Types of Data on GEO and TCGA
Bioconductor version: Release (3.19)
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")
):
Installation
To install this package, start R (version "4.4") 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 | 2.4.0 |
In Bioconductor since | BioC 3.17 (R-4.3) (1.5 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 |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | GeoTcgaData_2.4.0.tar.gz |
Windows Binary | GeoTcgaData_2.4.0.zip |
macOS Binary (x86_64) | GeoTcgaData_2.4.0.tgz |
macOS Binary (arm64) | GeoTcgaData_2.4.0.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 |