R Observatory: Metrics for ICDS version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2026-02-21. Its history is shown below.

Reason: issues were not corrected despite reminders

Details below reflect version 0.1.3, its last release before removal.

ICDS

0.1.3Package record

Identification of Cancer Dysfunctional Subpathway with Omics Data

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Junwei HanCRAN page ↗

Identify Cancer Dysfunctional Sub-pathway by integrating gene expression, DNA methylation and copy number variation, and pathway topological information. 1)We firstly calculate the gene risk scores by integrating three kinds of data: DNA methylation, copy number variation, and gene expression. 2)Secondly, we perform a greedy search algorithm to identify the key dysfunctional sub-pathways within the pathways for which the discriminative scores were locally maximal. 3)Finally, the permutation test was used to calculate statistical significance level for these key dysfunctional sub-pathways.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/ICDS/ICDS_0.1.3.tar.gz"
pkgFile <- "ICDS_0.1.3.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 (0.1.3) 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 0.1.3

READMEYes · 151 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 13includes a package overview page
Examples that run: 100%10 run in a plain check
Exported functions with examples: 91%
Documented parameters: 100%
Return-value docs: 91%
Help pages citing references: 8%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on52 r2u40 c2d4u

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.3.0

Imports (5)

igraph graphite metapmethodsorg.Hs.eg.db

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

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

Maintainer since 0.1.1 (2019)

Baotong Zheng

Author

Siyao Liu

Contributor

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2026-02-21
issues were not corrected despite reminders
R
R 4.5.0 released · 2025-04-11
0.1.3
record
2024-08-01 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-07-15
0.1.2
record
2021-07-15 · diff ↗
archivedRemoved from CRAN
2021-05-22
policy violation on Internet access
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
0.1.1
record
2019-01-25
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-01-25
Total releases: 3 / 7 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.3.0
Bundled data: 322 KB / 1 file

Cite

Cite this package

Run in R for the authors' entry:

citation("ICDS")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.3389/fgene.2019.00441.

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 ICDS version 0.1.3 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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