GeoTcgaData: Processing various types of data on GEO and TCGA

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.

Depends: R (≥ 3.6.0)
Imports: utils, data.table, magrittr, plyr, cqn, dplyr, topconfects
Suggests: knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr, clusterProfiler,, edgeR, limma, quantreg, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq
Published: 2022-09-23
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214 at>
License: Artistic-2.0
NeedsCompilation: no
Language: en-US
Materials: README
CRAN checks: GeoTcgaData results


Reference manual: GeoTcgaData.pdf
Vignettes: GeoTcgaData


Package source: GeoTcgaData_1.1.1.992.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): GeoTcgaData_1.0.2.tgz, r-oldrel (arm64): GeoTcgaData_0.2.5.tgz, r-release (x86_64): not available, r-oldrel (x86_64): GeoTcgaData_0.2.5.tgz
Old sources: GeoTcgaData archive


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