R Observatory: Metrics for rSEA version 2.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rSEA

2.1.2Package record

Simultaneous Enrichment Analysis

0packages dependsuggested by 1

6.3Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Mitra EbrahimpoorCRAN page ↗

SEA performs simultaneous feature-set testing for (gen)omics data. It tests the unified null hypothesis and controls the family-wise error rate for all possible pathways. The unified null hypothesis is defined as: "The proportion of true features in the set is less than or equal to a threshold." Family-wise error rate control is provided through use of closed testing with Simes test. There are some practical functions to play around with the pathways of interest.

Install

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

install.packages("rSEA", 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-rsea

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

# 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-rSEA

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-rSEA

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Mitra Ebrahimpoor<mitra.ebrahimpoor@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Mitra",
                    family = "Ebrahimpoor",
                    role = c("aut", "cre"),
                    email = "mitra.ebrahimpoor@gmail.com")
as necessary.

CRAN check page ↗

Slowest check: 1.7 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.2

READMEYes · 28 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 6includes a package overview page
Examples that run: 0%3 never run · 2 hold no code
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 100%

Vignettes (1)

rSEA R package HTML

How these are measured

Downloads

6.3K

CRAN downloads in the past year

Rank #9,855 · ~17/day · ~526/mo

Releases R versions

Daily download trend is not available in this view yet.

37330 days

1K90 days

6.3K1 year

Compare downloads with other packages →

Also on80 r2u4 autocran37 c2d4u

How downloads are counted

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing rSEA adds 19 packages (9 with compiled code, 15 MB of source tarballs). Heaviest: ggplot2 6.0 MB, Rcpp 1.8 MB, isoband 1.5 MB.

Depends (3)

R >= 2.10hommel ggplot2

Imports (0)

none

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

ReporterScore

How these are counted

Code & Tests

People & History

People (from the free-text Author field) (1)

Mitra Ebrahimpoor

Maintainer since 1.0 (2018)

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
2.1.2Latest
record
2024-06-12 · 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
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
2.1.1
record
2020-03-23 · diff ↗ ·
added 1 export
plotSEA
2.1.0
record
2019-10-06 · diff ↗
2.0.0
record
2019-10-03 · diff ↗ ·
removed 4 exports
sea.test, sea.top, set.test, tdphat

added 4 exports
SEA, setTDP, setTest, topSEA
R
R 3.6.0 released · 2019-04-26
1.0.1
record
2019-02-21 · diff ↗
1.0
record
2018-11-30
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-11-30
Total releases: 6 / 8 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Download size: 35 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rSEA")

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 rSEA version 2.1.2 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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