This package was removed from CRAN on 2026-06-24. Its history is shown below.

Reason: issues were not corrected despite reminders

Details below reflect version 0.3.3, its last release before removal.

SeqFeatR

0.3.3

A Tool to Associate FASTA Sequences and Features

0packages depend

3Kdownloads / year

–test coverage

–checks pass

Overview

About

Maintained by Bettina Budeus11 releasesCRAN page ↗

Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses, see Budeus (2016) doi:10.1371/journal.pone.0146409.

Install

R (source archive)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/SeqFeatR/SeqFeatR_0.3.3.tar.gz"
pkgFile <- "SeqFeatR_0.3.3.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 (0.3.3) 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-seqfeatr

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

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

ERROR2026-03-10
8 OK · 4 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 89%
Documented parameters: 100%
Return-value docs: 56%
References docs: 17%

Downloads

CRAN downloads in the past year

Rank #21,652 · ~8/day · ~247/mo

Releases R versions

Daily download trend is not available in this view yet.

030 days

55890 days

3K1 year

Compare downloads with other packages →

Also on103 r2u

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (5)

R >= 3.2.2tcltktcltk2 Biostrings plotrix

Imports (10)

plyr phangorn qvalue widgetTools calibrate ggplot2 R2jags coda scales ape

LinkingTo (0)

none

Suggests (1)

xtable

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Code Composition

R 8,680 (82%)Rd 1,317 (12%)Vignettes 344 (3%)Other 216 (2%)

Code characteristics

Cyclomatic complexity: 3.0 median / 117 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

131 1 exported

Complexity

5.4 avg / 117 max

Call network

131 nodes / 70 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (1)

Maintainer (1)

Bettina Budeus

Author, Maintainer

Authors (1)

Bettina Budeus

Author, Maintainer

Package Timeline

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

archivedRemoved from CRAN
2026-06-24
issues were not corrected despite reminders
R
R 4.6.0 released · 2026-04-24
0.3.3
2026-02-13 · 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
0.3.1
2019-04-12 · diff ↗
0.3
2018-11-30 · diff ↗
0.2.7
2018-05-18 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.2.6
2018-03-06 · diff ↗
R
R 3.4.0 released · 2017-04-21

Show 9 earlier events

0.2.4
2016-10-17 · diff ↗
0.2.3
2016-05-25 · diff ↗
R
R 3.3.0 released · 2016-05-03
0.2.2
2016-03-25 · diff ↗
0.2.0
2015-08-20 · diff ↗
R
R 3.2.0 released · 2015-04-16
0.1.7
2015-02-11 · diff ↗
0.1.5
2014-06-10
R
R 3.1.0 released · 2014-04-10

Package metadata

Total releases: 11
License: GPL (>= 3) OSI
Minimum R: ≥ 3.2.2
Download size: 863 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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