R Observatory: Metrics for samr version 3.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

samr

3.0.1Package record

SAM: Significance Analysis of Microarrays

1packages dependsuggested by 1

21.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Rob TibshiraniCRAN page ↗

Significance Analysis of Microarrays for differential expression analysis, RNAseq data and related problems.

Install

R (CRAN)Ubuntu (r2u)

install.packages("samr", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-samr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.0 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.0.1

READMEYes · 97 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 15 (1 internal)
Examples that run: 93%13 run in a plain check · 1 never run
Exported functions with examples: 93%
Documented parameters: 90%
Return-value docs: 53%
Help pages citing references: 93%

How these are measured

Downloads

21.2K

CRAN downloads in the past year

Rank #3,299 · ~58/day · ~1.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.4K30 days

3.4K90 days

21.2K1 year

Compare downloads with other packages →

Also on548 r2u2.5K bioconda75 c2d4u

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing samr adds 41 packages (26 with compiled code, 41 MB of source tarballs). Heaviest: stringi 11 MB, bslib 5.6 MB, promises 3.1 MB. 1 more not on CRAN is not measured.

Depends (0)

none

Imports (6)

impute matrixStats shiny shinyFiles openxlsx GSA

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

SMDIC

Suggests, most downloaded first

st

How these are counted

Code & Tests

People & History

People (5)

Rob Tibshirani

Author, Maintainer · added in 3.0.1

G. Chu

Author

Jun Li

Author · added in 2.0

Balasubramanian Narasimhan

Author

Michael J. Seo

Author · added in 3.0

Maintainer since 1.00 (2005)

Listed in earlier versions (3)

Show 3 peopleHide 3 people

T. Hastie

no longer listed · 1.00 to 1.28

R. Tibshirani

no longer listed · 1.00 to 3.0

Seo

no longer listed · 3.0.1

Releases (11)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
3.0.1Latest
record
2026-04-10 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
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
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
unarchivedReturned to CRAN
2018-10-16
3.0
record
2018-10-16 · diff ↗ ·
removed 6 exports
samr.xl.build.data, samr.xl.error.trace, samr.xl.compute.plot.xy, samr.xl.impute.data, samr.xl.parse.survival, samr.xl.parse.patterndiscovery

added 1 export
runSAM
archivedRemoved from CRAN
2018-07-20
check problems were not corrected despite reminders
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

Show 26 earlier eventsHide 26 earlier events

R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
2.0
record
2011-06-29 · diff ↗ ·
added 6 exports
SAM, SAMseq, plot.SAMoutput, print.SAMoutput, samr.norm.data, samr.estimate.depth
R
R 2.13.0 released · 2011-04-13
R
R 2.12.0 released · 2010-10-15
R
R 2.11.0 released · 2010-04-22
1.28
record
2010-03-13 · diff ↗
1.27
record
2010-01-04 · diff ↗
R
R 2.10.0 released · 2009-10-26
R
R 2.9.0 released · 2009-04-17
R
R 2.8.0 released · 2008-10-20
1.26
record
2008-09-28 · diff ↗
R
R 2.7.0 released · 2008-04-22
R
R 2.6.0 released · 2007-10-03
1.25
record
2007-06-07 · diff ↗
R
R 2.5.0 released · 2007-04-24
1.24
record
2007-04-19 · diff ↗ ·
added 2 exports
samr.pvalues.from.perms, samr.tail.strength
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
1.20
record
2005-10-05 · diff ↗ ·
added 5 exports
check.format, ttest.func, samr.assess.samplesize, samr.assess.samplesize.plot, samr.xl.impute.data
1.01
record
2005-07-21 · diff ↗
1.00
record
2005-06-01
R
R 2.1.0 released · 2005-04-18

Package metadata

First published: 2005-06-01
Total releases: 11 / 21 yrs
License: LGPL
Download size: 3.5 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("samr")

Format

Tibshirani, R., Chu, G., Li, J., Narasimhan, B., & Seo, M. J. (2026). samr: SAM: Significance Analysis of Microarrays (Version 3.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.samr

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 samr version 3.0.1 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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