R Observatory: Metrics for dnet version 1.1.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2024-01-30. Its history is shown below.

Reason: email to the maintainer is undeliverable

Details below reflect version 1.1.7, its last release before removal.

dnet

1.1.7Package record

Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Hai FangCRAN page ↗GitHub ↗Website ↗

The focus of the dnet by Fang and Gough (2014) doi:10.1186/s13073-014-0064-8 is to make sense of omics data (such as gene expression and mutations) from different angles including: integration with molecular networks, enrichments using ontologies, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes/genes are labelled with informative data (such as the significant levels of differential expression or survival risks). To help make sense of identified gene networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including: human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for calculating semantic similarity between ontology terms (and between genes) and for calculating network affinity based on random walk; both can be done via high-performance parallel computing.

Install

R (source archive)pak (dev)

url <- "https://cran.r-project.org/src/contrib/Archive/dnet/dnet_1.1.7.tar.gz"
pkgFile <- "dnet_1.1.7.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 (1.1.7) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("hfang-bristol/dnet")

Development version from hfang-bristol/dnet. Installs pak first if it is not already available.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.7

READMENoVignettesNoNEWSYes · 0% structuredCitation fileYes · cites a publicationWebsiteYes

Help pages: 43
Examples that run: 44%19 run in a plain check · 16 never run · 8 hold no code
Exported functions with examples: 100%
Documented parameters: 94%
Return-value docs: 100%
Help pages citing references: 5%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on110 r2u1K bioconda44 c2d4u

How downloads are counted

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.1.0igraph supraHex

Imports (3)

graph RgraphvizMatrix

LinkingTo (0)

none

Suggests (5)

limmasurvivalforeach doParallel Biobase

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 (2)

Hai Fang

Contributor

Julian Gough

Contributor

Maintainer since 0.99.0 (2014)

Releases (19)

Pick two releases to compare their code metrics.

R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2024-01-30
email to the maintainer is undeliverable
R
R 4.3.0 released · 2023-04-21
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
1.1.7
record
2020-02-20 · diff ↗
1.1.6
record
2020-01-23 · diff ↗
1.1.5
record
2019-10-18 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1.4
record
2018-08-10 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.1.3
record
2018-02-23 · diff ↗
1.1.2
record
2018-01-19 · diff ↗
1.1.1
record
2017-07-09 · diff ↗
R
R 3.4.0 released · 2017-04-21

Show 16 earlier eventsHide 16 earlier events

1.0.10
record
2017-01-27 · diff ↗
1.0.9
record
2016-05-31 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.0.8
record
2016-04-01 · diff ↗
1.0.7
record
2015-07-17 · diff ↗ ·
added 2 exports
dFunArgs, visNetAnimate
R
R 3.2.0 released · 2015-04-16
1.0.6
record
2014-09-17 · diff ↗
1.0.5
record
2014-07-02 · diff ↗
1.0.4
record
2014-06-05 · diff ↗
1.0.3
record
2014-05-19 · diff ↗ ·
added 6 exports
dCheckParallel, dDAGancestor, dDAGgeneSim, dDAGtermSim, dRWRcontact, dRWRpipeline
1.0.2
record
2014-04-30 · diff ↗ ·
added 2 exports
dEnricherView, dRDataLoader
1.0.1
record
2014-04-21 · diff ↗ ·
removed 5 exports
visColoralpha, visColormap, visHeatmap, visHeatmapAdv, visTreeBootstrap

added 1 export
visBoxplotAdv
R
R 3.1.0 released · 2014-04-10
1.0.0
record
2014-04-09 · diff ↗ ·
added 8 exports
dDAGannotate, dDAGinduce, dDAGlevel, dDAGreverse, dDAGroot, dDAGtip, dEnricher, visDAG
0.99.0
record
2014-03-25
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2014-03-25
Total releases: 19 / 12 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.1.0
Bundled data: 396 KB / 3 files

Cite

Cite this package

Run in R for the authors' entry:

citation("dnet")

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

It points to 10.1186/s13073-014-0064-8.

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 dnet version 1.1.7 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →