This package was removed from CRAN on 2023-05-05. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 1.0-11-0, its last release before removal.

QuasiSeq

1.0-11-0

Analyzing RNA Sequencing Count Tables Using Quasi-Likelihood

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Steve Lund11 releasesCRAN page ↗

Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with 'QL', 'QLShrink' and 'QLSpline' methods described by Lund, Nettleton, McCarthy, and Smyth (2012) DOI:10.1515/1544-6115.1826. Report bias-reduced estimates of log fold changes.

Install

R (source archive)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/QuasiSeq/QuasiSeq_1.0-11-0.tar.gz"
pkgFile <- "QuasiSeq_1.0-11-0.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 (1.0-11-0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-quasiseq

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 1.63

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 78%
Documented parameters: 87%
Return-value docs: 100%
References docs: 40%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on340 r2u18 c2d4u

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (6)

edgeRmgcvpracmautilsgrDevicesgraphics

LinkingTo (0)

none

Suggests (2)

BB nleqslv

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Steve Lund

Author, Maintainer

Authors (5)

Steve Lund

Author, Maintainer

Long Qu

Author, Contributor · added in 1.0-3

Klirk Bhasavanich

Author · added in 1.0-10-1

Ian Marschner

Author · added in 1.0-7

R Core Team

Author · added in 1.0-7

Contributors (1)

Long Qu

Author, Contributor · added in 1.0-3

Package Timeline

11 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2023-05-05
issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
1.0-11-0
2022-08-15 · diff ↗
unarchivedReturned to CRAN
2022-08-15
archivedRemoved from CRAN
2022-05-07
installation issues were not corrected in time
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
1.0-10-2
2018-05-10 · diff ↗
unarchivedReturned to CRAN
2018-05-10
R
R 3.5.0 released · 2018-04-23
archivedRemoved from CRAN
2017-12-19
it depends on 'uniqueAtomMat', which was archived
1.0-10-1
2017-07-09 · diff ↗
R
R 3.4.0 released · 2017-04-21

Show 13 earlier events

R
R 3.3.0 released · 2016-05-03
1.0-8
2015-05-14 · diff ↗
1.0-7
2015-05-13 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.0-6
2015-02-02 · diff ↗
1.0-5
2015-01-05 · diff ↗
1.0-4
2014-04-14 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.0-3
2014-02-06 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.0-2
2012-05-07 · diff ↗
1.0-1
2012-04-14
R
R 2.15.0 released · 2012-03-30

Package metadata

Total releases: 11
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0.0
Bundled data: 270 KB / 1 file
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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