R Observatory: Metrics for graphite version 1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2011-07-05. Its history is shown below.

Reason: This package is now available from Bioconductor only, see <https://www.bioconductor.org/packages/release/bioc/html/graphite.html>

Details below reflect version 1.1, its last release before removal.

graphite

1.1Package record

GRAPH Interaction from pathway Topological Environment

2packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Gabriele SalesCRAN page ↗

Graph objects from pathway topology derived from NCI, KEGG, Biocarta and Reactome databases.

Install

BioconductorR (source archive)

BiocManager::install("graphite")

Installs the current Bioconductor release. Requires the BiocManager package.

url <- "https://cran.r-project.org/src/contrib/Archive/graphite/graphite_1.1.tar.gz"
pkgFile <- "graphite_1.1.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 (1.1) 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 1.1

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 12
Examples that run: 83%5 run in a plain check · 1 never run
Exported functions with examples: 86%
Documented parameters: 100%
Return-value docs: 43%
Help pages citing references: 33%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on1.5K r2u10.8K bioconda47 c2d4u

How downloads are counted

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (5)

R >= 2.10methodsgraph AnnotationDbi org.Hs.eg.db

Imports (0)

none

LinkingTo (0)

none

Suggests (5)

DEGraph hgu133plus2.db RCytoscape SPIA topologyGSA

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

–indirect (not tracked)

Imports 2

Depends, Imports or LinkingTo, most downloaded first

SEMgraph netgsa

How these are counted

Code & Tests

Datasets

People & History

People (3)

Gabriele Sales

Contributor

Enrica Calura

Contributor

Chiara Romualdi

Contributor

Maintainer since 1.0 (2011)

Releases (2)

Pick two releases to compare their code metrics.

R
R 2.14.0 released · 2011-10-31
1.1archived
2011-07-05 · diff ↗
This package is now available from Bioconductor only, see <https://www.bioconductor.org/packages/release/bioc/html/graphite.html>
1.1
record
2011-05-27 · diff ↗ ·
removed 1 export
pattern:^[^\\.]

added 7 exports
convertIdentifiers, pathwayGraph, cytoscapePlot, prepareSPIA, runSPIA, runDEGraph, runTopologyGSA
1.0
record
2011-05-27
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-05-27
Total releases: 2 / 15 yrs
License: AGPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 829 KB / 1 file

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("graphite")

Format

Sales, G., Calura, E., & Romualdi, C. (n.d.). graphite: GRAPH Interaction from pathway Topological Environment (Version 1.1) [Computer software]. Retrieved October 19, 2026, from https://CRAN.R-project.org/package=graphite

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 graphite version 1.1 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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