R Observatory: Metrics for AbsFilterGSEA version 1.5.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2020-10-11. Its history is shown below.

Reason: check problems were not corrected in time

Details below reflect version 1.5.1, its last release before removal.

AbsFilterGSEA

1.5.1Package record

Improved False Positive Control of Gene-Permuting GSEA with Absolute Filtering

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Sora YoonCRAN page ↗

Gene-set enrichment analysis (GSEA) is popularly used to assess the enrichment of differential signal in a pre-defined gene-set without using a cutoff threshold for differential expression. The significance of enrichment is evaluated through sample- or gene-permutation method. Although the sample-permutation approach is highly recommended due to its good false positive control, we must use gene-permuting method if the number of samples is small. However, such gene-permuting GSEA (or preranked GSEA) generates a lot of false positive gene-sets as the inter-gene correlation in each gene set increases. These false positives can be successfully reduced by filtering with the one-tailed absolute GSEA results. This package provides a function that performs gene-permuting GSEA calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/AbsFilterGSEA/AbsFilterGSEA_1.5.1.tar.gz"
pkgFile <- "AbsFilterGSEA_1.5.1.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 (1.5.1) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.5.1

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 2
Examples that run: 100%2 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 100%

How these are measured

Downloads

AbsFilterGSEA Releases R versions

Daily download trend is not available in this view yet.

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How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (5)

Rcpp BiobasestatsDESeq limma

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Sora Yoon

Contributor

Maintainer since 0.1 (2016)

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.1.0 released · 2021-05-18
archivedRemoved from CRAN
2020-10-11
check problems were not corrected in time
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.5.1
record
2017-09-21 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.5
record
2016-08-26 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.2.1
record
2016-04-04 · diff ↗
1.2
record
2016-03-30 · diff ↗
1.0
record
2016-03-16 · diff ↗
0.1
record
2016-01-04
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-01-04
Total releases: 6 / 10 yrs
License: GPL-2 OSI
Bundled data: 79 KB / 1 file

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("AbsFilterGSEA")

Format

Yoon, S. (n.d.). AbsFilterGSEA: Improved False Positive Control of Gene-Permuting GSEA with Absolute Filtering (Version 1.5.1) [Computer software]. Retrieved October 27, 2026, from https://CRAN.R-project.org/package=AbsFilterGSEA

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 AbsFilterGSEA version 1.5.1 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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