R Observatory: Metrics for ESEA version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2022-06-20. Its history is shown below.

Reason: check problems were not corrected despite reminders

Details below reflect version 1.0, its last release before removal.

ESEA

1.0Package record

ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Xinrui ShiCRAN page ↗

The package can identify the dysregulated canonical pathways by investigating the changes of biological relationships of pathways in the context of gene expression data. (1) The ESEA package constructs a background set of edges by extracting pathway structure (e.g. interaction, regulation, modification, and binding etc.) from the seven public databases (KEGG; Reactome; Biocarta; NCI; SPIKE; HumanCyc; Panther) and the edge sets of pathways for each of the above databases. (2) The ESEA package can can quantify the change of correlation between genes for each edge based on gene expression data with cases and controls. (3) The ESEA package uses the weighted Kolmogorov-Smirnov statistic to calculate an edge enrichment score (EES), which reflects the degree to which a given pathway is associated the specific phenotype. (4) The ESEA package can provide the visualization of the results.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/ESEA/ESEA_1.0.tar.gz"
pkgFile <- "ESEA_1.0.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 (1.0) 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 1.0

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 14 (1 internal)
Examples that run: 0%9 never run
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 14%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on55 r2u5 autocran

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (4)

R >= 2.10igraph XML parmigene

Imports (0)

none

LinkingTo (0)

none

Suggests (2)

Matrixgraph

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 (3)

Junwei Han

Contributor

Xinrui Shi

Contributor

Chunquan Li

Contributor

Maintainer since 1.0 (2015)

Releases (1)

R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2022-06-20
check problems were not corrected despite reminders
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
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
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
1.0
record
2015-01-22
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2015-01-22
Total releases: 1 / 11 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Bundled data: 1.8 MB / 2 files

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ESEA")

Format

Han, J., Shi, X., & Li, C. (n.d.). ESEA: ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis (Version 1.0) [Computer software]. Retrieved October 27, 2026, from https://CRAN.R-project.org/package=ESEA

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 ESEA version 1.0 [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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