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 (3.21)
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:
Maintainer: Erqiang Hu <13766876214 at 163.com>
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")| GeoTcgaData | HTML | R Script |
| Reference Manual |
Details
| biocViews | ATACSeq, CopyNumberVariation, DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, MethylationArray, Microarray, RNASeq, SNP, Software |
| Version | 2.7.0 |
| 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 |
| 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_2.7.0.tar.gz |
| Windows Binary (x86_64) | GeoTcgaData_2.7.0.zip (64-bit only) |
| macOS Binary (x86_64) | GeoTcgaData_2.7.0.tgz |
| macOS Binary (arm64) | GeoTcgaData_2.7.0.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 |