R Observatory: Metrics for mseq version 1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2014-12-22. Its history is shown below.

Reason: the maintainer was unable to follow the procedures to fix the maintainer email address

Details below reflect version 1.2, its last release before removal.

mseq

1.2Package record

Modeling non-uniformity in short-read rates in RNA-Seq data

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Jun LiCRAN page ↗

This package implements all the methods in the paper "Modeling non-uniformity in short-read rates in RNA-Seq data". Especially, it implements both the iterative glm procedure for the Poisson linear model and the training procedure of the MART model. The cross-validation for both of the methods is also implemented. Version 1.1 and later also implements the Poisson linear model with dinucleotide composition. Version 1.2 corrected a bug in expData.R. This bug leads to mis-labeled lines in plotCoef.R, but will not change other parts like training, testing, or cross-validation.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/mseq/mseq_1.2.tar.gz"
pkgFile <- "mseq_1.2.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 (1.2) 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 1.2

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 23includes a package overview page
Examples that run: 100%17 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 13%

How these are measured

Downloads

mseq Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

How downloads are counted

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (2)

R >= 2.5gbm

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

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 (1)

Jun Li

Contributor

Maintainer since 1.0 (2009)

Releases (3)

Pick two releases to compare their code metrics.

R
R 3.2.0 released · 2015-04-16
archivedRemoved from CRAN
2014-12-22
the maintainer was unable to follow the procedures to fix the maintainer email address
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
1.2
record
2011-09-07 · diff ↗
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
1.1
record
2010-01-27 · diff ↗ ·
added 4 exports
expData2nt, glmPred2nt, iterGlmCV2nt, iterGlm2nt
1.0
record
2009-11-30
R
R 2.10.0 released · 2009-10-26

Package metadata

First published: 2009-11-30
Total releases: 3 / 17 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.5
Bundled data: 17 KB / 1 file

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("mseq")

Format

Li, J. (n.d.). mseq: Modeling non-uniformity in short-read rates in RNA-Seq data (Version 1.2) [Computer software]. Retrieved October 26, 2026, from https://CRAN.R-project.org/package=mseq

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 mseq version 1.2 [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.

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