R Observatory: Metrics for seqgendiff version 1.2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

seqgendiff

1.2.4Package record

RNA-Seq Generation/Modification for Simulation

0packages depend

3.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by David GerardCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 1.2.4

Adds back seqgendiff::EigenDiff() since cate is no longer on CRAN.
Removes cate as imports because it is not longer on CRAN.

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-27
ERROR12 OK, 1 ERROR2026-06-21
OK13 OK2026-06-09

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.4

READMEYes · 393 wordsVignettesYes · 2 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 1.2.4Citation fileYes · cites a publication

Help pages: 18includes a package overview page
Examples that run: 85%11 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 72%

Vignettes (2)

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #7,823 · ~9/day · ~285/mo

Releases R versions

Daily download trend is not available in this view yet.

52830 days

1.1K90 days

3.4K1 year

Compare downloads with other packages →

Also on126 r2u39 c2d4u

How downloads are counted

Repository

dcgerard/seqgendiff ↗Account: dcgerard

11Stars

2Forks

3Open issues

0Open PRs

4Releases

96Commits

1Commit identities

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

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-12-07 · 102026-07-07 · 11

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/dcgerard/seqgendiff on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Code of conduct

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2024-05-15

Coverage (1)

Coverage reporting (Codecov)

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing seqgendiff adds 7 packages (6 with compiled code, 3.9 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppArmadillo 1.0 MB, clue 727 KB. 1 more not on CRAN is not measured.

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.

How these are counted

Code & Tests

People & History

People (1)

David Gerard

Author, Maintainer since 1.1.0 (2019)

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.2.4Latest
record
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
record
2022-02-19 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.2.2
record
2020-05-24 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.2.1
record
2020-02-24 · diff ↗
1.1.1
record
2019-09-10 · diff ↗
1.1.0
record
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

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("seqgendiff")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1186/s12859-020-3450-9.

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 v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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