SimSeq

1.4.0

Nonparametric Simulation of RNA-Seq Data

0packages depend

3Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Samuel BenidtFirst published 2014-02-184 releasesCRAN page ↗

RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model. This testing strategy can result in an overly optimistic view of the performance of an RNA-seq analysis method. We develop a data-based simulation algorithm for RNA-seq data. The vector of read counts simulated for a given experimental unit has a joint distribution that closely matches the distribution of a source RNA-seq dataset provided by the user. Users control the proportion of genes simulated to be differentially expressed (DE) and can provide a vector of weights to control the distribution of effect sizes. The algorithm requires a matrix of RNA-seq read counts with large sample sizes in at least two treatment groups. Many datasets are available that fit this standard.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

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

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

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-simseq

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-SimSeq

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-SimSeq

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 49 s · r-release-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

None

Vignettes

README

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

CRAN downloads in the past year

Rank #18,252 · ~8/day · ~248/mo

By source Releases R versions

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24030 days

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Also on182 r2u10 autocran

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (1)

R >= 2.10.0

Imports (1)

fdrtool

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

Rd 599 (59%)R 410 (41%)

Code characteristics

Cyclomatic complexity: 16.0 median / 89 max
Documented parameters: 100%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

3 3 exported

Complexity

36.7 avg / 89 max

Call network

3 nodes / 3 edges

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

Call graph

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Lowest coverage

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

People & History

People (0)

Author records are not tracked yet for this package.

Release timeline

4 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
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
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.4.0Latest
2015-11-23 · current release · diff ↗
R
R 3.2.0 released · 2015-04-16
1.3.0
2015-03-07 · diff ↗
1.2.0
2014-12-10 · diff ↗
R
R 3.1.0 released · 2014-04-10

Show 2 earlier events

1.0.0
2014-02-18
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2014-02-18
Total releases: 4 / 12 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10.0
Bundled data: 4.2 MB / 2 files
Download size: 4.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet