R Observatory: Metrics for ggcoverage version 0.7.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2023-11-16. Its history is shown below.

Reason: issues were not corrected in time. Including not using suggested packages conditionally

Details below reflect version 0.7.1, its last release before removal.

ggcoverage

0.7.1

Visualize Genome Coverage with Various Annotations

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Yabing Song2 releasesCRAN page ↗

The goal of 'ggcoverage' is to simplify the process of visualizing genome coverage. It contains functions to load data from BAM, BigWig or BedGraph files, create genome coverage plot, add various annotations to the coverage plot, including base and amino acid annotation, GC annotation, gene annotation, transcript annotation, ideogram annotation and peak annotation.

Install

R (source archive)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/ggcoverage/ggcoverage_0.7.1.tar.gz"
pkgFile <- "ggcoverage_0.7.1.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 (0.7.1) 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-ggcoverage

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

25

Dependencies · direct

Documentation

READMEYes · 487 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 96%
Return-value docs: 100%
References docs: 0%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on98 r2u237 bioconda

Dependencies

Declared dependencies

26 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (25)

dplyr GenomicRanges ggbio ggh4x ggplot2 ggrepelgrDevicesIRanges magrittr patchwork RColorBrewer rlang Rsamtools rtracklayer scalesstatsutilsmethodsGenomeInfoDb S4Vectors Biostrings BSgenome GenomicAlignments reshape2 seqinr

LinkingTo (0)

none

Suggests (6)

rmarkdown knitr BiocStyle htmltools BSgenome.Hsapiens.UCSC.hg19graphics

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Yabing Song

Author, Maintainer

Authors (1)

Yabing Song

Author, Maintainer

Package Timeline

2 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
2023-11-16
issues were not corrected in time Including not using suggested packages conditionally
R
R 4.3.0 released · 2023-04-21
0.7.1
2022-09-06 · diff ↗
0.7.0
2022-08-18
R
R 4.2.0 released · 2022-04-22

Package metadata

Total releases: 2
License: MIT + file LICENSE OSI
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ggcoverage")

Format

Song, Y. (n.d.). ggcoverage: Visualize Genome Coverage with Various Annotations (Version 0.7.1) [Computer software]. Retrieved August 14, 2026, from https://CRAN.R-project.org/package=ggcoverage

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 ggcoverage version 0.7.1 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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