R Observatory: Metrics for GeoTcgaData version 1.1.1.992

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2022-11-19. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 1.1.1.992, its last release before removal.

GeoTcgaData

1.1.1.992

Processing various types of data on GEO and TCGA

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Erqiang Hu13 releasesCRAN page ↗

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.

Install

BioconductorR (source archive)Ubuntu (r2u)openSUSE (OBS)

BiocManager::install("GeoTcgaData")

Installs the current Bioconductor release. Requires the BiocManager package.

url <- "https://cran.r-project.org/src/contrib/Archive/GeoTcgaData/GeoTcgaData_1.1.1.992.tar.gz"
pkgFile <- "GeoTcgaData_1.1.1.992.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.1.1.992) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-geotcgadata

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-GeoTcgaData

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

7

Dependencies · direct

Documentation

READMEYes · 972 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 71%
Documented parameters: 100%
Return-value docs: 64%
References docs: 0%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on125 r2u14 autocran554 bioconda

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (7)

utilsdata.table magrittr plyr cqn dplyr topconfects

LinkingTo (0)

none

Suggests (16)

knitr rmarkdown DESeq2 S4Vectors ChAMP impute tidyr clusterProfiler org.Hs.eg.db edgeR limma quantreg minfi IlluminaHumanMethylation450kanno.ilmn12.hg19 dearseq NOISeq

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Erqiang Hu

Author, Maintainer

Authors (1)

Erqiang Hu

Author, Maintainer

Package Timeline

13 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2022-11-19
issues were not corrected in time
1.1.1.992
2022-09-23 · diff ↗
1.1.1
2022-08-12 · diff ↗
1.1.0
2022-08-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.2
2021-10-24 · diff ↗
1.0.1
2021-08-01 · diff ↗
1.0.0.1
2021-07-26 · diff ↗
1.0.0
2021-07-16 · diff ↗
0.2.5
2021-06-06 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.2.4
2020-06-09 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.2.3
2020-02-22 · diff ↗
0.2.2
2020-01-07 · diff ↗

Show 3 earlier events

0.2.0
2019-09-23 · diff ↗
0.1.0
2019-09-16
R
R 3.6.0 released · 2019-04-26

Package metadata

Total releases: 13
License: Artistic-2.0 OSI
Minimum R: ≥ 3.6.0
Bundled data: 388 KB / 7 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GeoTcgaData")

Format

Hu, E. (n.d.). GeoTcgaData: Processing various types of data on GEO and TCGA (Version 1.1.1.992) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=GeoTcgaData

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for GeoTcgaData version 1.1.1.992 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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