R Observatory: Metrics for seqgendiff version 1.2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

seqgendiff

1.2.4

RNA-Seq Generation/Modification for Simulation

0packages depend

3.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by David GerardFirst published 2019-08-056 releasesCRAN page ↗GitHub ↗

Generates/modifies RNA-seq data for use in simulations. We provide a suite of functions that will add a known amount of signal to a real RNA-seq dataset. The advantage of using this approach over simulating under a theoretical distribution is that common/annoying aspects of the data are more preserved, giving a more realistic evaluation of your method. The main functions are select_counts(), thin_diff(), thin_lib(), thin_gene(), thin_2group(), thin_all(), and effective_cor(). See Gerard (2020) doi:10.1186/s12859-020-3450-9 for details on the implemented methods.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("dcgerard/seqgendiff")

Development version from dcgerard/seqgendiff. Installs pak first if it is not already available.

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-seqgendiff

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

13OK

Slowest check: 4.1 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.23

not tracked

Coverage

100%

Documentation · exports

6

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 393 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 85%
Documented parameters: 98%
Return-value docs: 100%
References docs: 72%

Downloads

3.9K

CRAN downloads in the past year

Rank #12,210 · ~11/day · ~322/mo

Releases R versions

Daily download trend is not available in this view yet.

26230 days

81490 days

3.9K1 year

Compare downloads with other packages →

Also on119 r2u22 c2d4u

Repository

GitHub ↗ dcgerard/seqgendiff

11Stars

2Forks

3Open issues

0Open PRs

4Releases

96Commits

1Contributors

License GPL-3.0 · 96 commits · Last activity 2024-05-15 · 0% stars, 30d

Stars over time

2024-12-07 · 102026-07-07 · 11

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/dcgerard/seqgendiff on 2026-08-16.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (6)

assertthat irlba sva pdist matchingR clue

LinkingTo (0)

none

Suggests (10)

covr testthat SummarizedExperiment DESeq2 knitr rmarkdown airway limma qvalue edgeR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

David Gerard

Author, Maintainer

Authors (1)

David Gerard

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.2.4Latest
2024-05-15 · current release · diff ↗
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
1.2.3
2022-02-19 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.2.2
2020-05-24 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.2.1
2020-02-24 · diff ↗
1.1.1
2019-09-10 · diff ↗
1.1.0
2019-08-05
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-05
Total releases: 6 / 7 yrs
License: GPL-3 OSI
Download size: 288 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("seqgendiff")

Format

Gerard, D. (2024). seqgendiff: RNA-Seq Generation/Modification for Simulation (Version 1.2.4) [Computer software]. https://doi.org/10.32614/CRAN.package.seqgendiff

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 seqgendiff version 1.2.4 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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