R Observatory: Metrics for qvalue version 1.26.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2011-04-26. Its history is shown below.

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

Details below reflect version 1.26.0, its last release before removal.

qvalue

1.26.0Package record

Q-value estimation for false discovery rate control

18packages dependsuggested by 16

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by John D. StoreyCRAN page ↗

This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

Install

BioconductorR (source archive)

BiocManager::install("qvalue")

Installs the current Bioconductor release. Requires the BiocManager package.

url <- "https://cran.r-project.org/src/contrib/Archive/qvalue/qvalue_1.26.0.tar.gz"
pkgFile <- "qvalue_1.26.0.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 (1.26.0) 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 1.26.0

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 6
Examples that run: 0%5 never run
Exported functions with examples: 100%
Documented parameters: 88%
Return-value docs: 100%
Help pages citing references: 50%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on9.4K r2u130.1K bioconda

How downloads are counted

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

graphicsgrDevicesstatstcltk

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

18direct

–indirect (not tracked)

Depends 4 · Imports 14

Suggested by 16

Show all 34 packagesHide all 34 packages

Depends, Imports or LinkingTo, most downloaded first

isva HDMT glmmSeq jaccard AEenrich NBPSeq cp4p ssizeRNA shinyExprPortal groupedSurv STAREG ReAD fdrDiscreteNull cancerGI medScan sffdr BonEV TFactSR

Suggests, most downloaded first

enrichit mutoss wrMisc dartR dartR.base dartR.popgen jackstraw volcano3D seqgendiff DGEobj.utils easylabel Rediscover readyomics multiDEGGs BootstrapQTL DANDELION

How these are counted

Code & Tests

Datasets

People & History

People (3)

Alan Dabney

Contributor

John D. Storey

Contributor

with assistance from Gregory R. Warnes

Contributor

Maintainer since 1.1 (2004)

Releases (7)

Pick two releases to compare their code metrics.

R
R 2.14.0 released · 2011-10-31
1.26.0archived
2011-04-26 · diff ↗
This package is now available from Bioconductor only, see <https://www.bioconductor.org/packages/release/bioc/html/qvalue.html>
1.26.0
record
2011-04-14 · diff ↗
R
R 2.13.0 released · 2011-04-13
1.24.0
record
2010-10-18 · diff ↗ ·
added 7 exports
plot.qvalue, qplot, qsummary, qvalue, qvalue.gui, qwrite, summary.qvalue
R
R 2.12.0 released · 2010-10-15
1.22.0
record
2010-04-22 · diff ↗
R
R 2.11.0 released · 2010-04-22
1.20.0
record
2009-11-12 · diff ↗
R
R 2.10.0 released · 2009-10-26
1.18.0
record
2009-04-21 · diff ↗
R
R 2.9.0 released · 2009-04-17
1.1.1
record
2009-02-24 · diff ↗
R
R 2.8.0 released · 2008-10-20
R
R 2.7.0 released · 2008-04-22
R
R 2.6.0 released · 2007-10-03

Show 7 earlier eventsHide 7 earlier events

R
R 2.5.0 released · 2007-04-24
R
R 2.4.0 released · 2006-10-03
R
R 2.3.0 released · 2006-04-24
R
R 2.2.0 released · 2005-10-06
R
R 2.1.0 released · 2005-04-18
1.1
record
2004-10-09
R
R 2.0.0 released · 2004-10-04

Package metadata

First published: 2004-10-09
Total releases: 7 / 22 yrs
License: LGPL
Bundled data: 23 KB / 1 file

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("qvalue")

Format

Dabney, A., Storey, J. D., & Warnes, w. a. f. G. R. (n.d.). qvalue: Q-value estimation for false discovery rate control (Version 1.26.0) [Computer software]. Retrieved October 19, 2026, from https://CRAN.R-project.org/package=qvalue

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 qvalue version 1.26.0 [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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