R Observatory: Metrics for metevalue version 0.2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

metevalue

0.2.4Package record

E-Value in the Omics Data Association Studies

0packages depend

2.7Kdownloads / year

60.5%test coverage

13/13flavors OK

Overview

About

Maintained by Yifan YangCRAN page ↗

In the omics data association studies, it is common to conduct the p-value corrections to control the false significance. Beyond the P-value corrections, E-value is recently studied to facilitate multiple testing correction based on V. Vovk and R. Wang (2021) doi:10.1214/20-AOS2020. This package provides E-value calculation for DNA methylation data and RNA-seq data. Currently, five data formats are supported: DNA methylation levels using DMR detection tools (BiSeq, DMRfinder, MethylKit, Metilene and other DNA methylation tools) and RNA-seq data. The relevant references are listed below: Katja Hebestreit and Hans-Ulrich Klein (2022) doi:10.18129/B9.bioc.BiSeq; Altuna Akalin et.al (2012) doi:10.18129/B9.bioc.methylKit.

Install

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

install.packages("metevalue", 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-metevalue

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-metevalue

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-metevalue

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

13OK

CRAN check page ↗

Slowest check: 2.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.4

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 22
Examples that run: 50%7 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran) · 5 hold no code
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 9%

Vignettes (1)

E-value in DNA methylation studies

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #17,279 · ~7/day · ~227/mo

Releases R versions

Daily download trend is not available in this view yet.

30930 days

73490 days

2.7K1 year

Compare downloads with other packages →

Also on93 r2u3 autocran

How downloads are counted

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing metevalue adds 31 packages (16 with compiled code, 15 MB of source tarballs). Heaviest: RSQLite 4.2 MB, GPArotation 1.6 MB, psych 1.1 MB.

Depends (4)

R >= 3.5.0sqldf psych dplyr

Imports (0)

none

LinkingTo (0)

none

Suggests (6)

rmarkdown prettydoc knitr ggplot2 tidyr testthat (>= 3.0.0)

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Yifan Yang

Haoyuan Liu

Author

Xiaoqing Pan

Author

Releases (5)

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
R
R 4.4.0 released · 2024-04-24
0.2.4Latest
record
2023-05-26 · current release · diff ↗ ·
removed 1 export
varevalue.signle_general

added 1 export
varevalue.single_general
0.2.2
record
2023-05-18 · diff ↗ ·
added 2 exports
varevalue.signle_general, metevalue.RNA_general
R
R 4.3.0 released · 2023-04-21
0.1.14
record
2023-03-28 · diff ↗
0.1.13
record
2022-11-21 · diff ↗
0.1.10
record
2022-10-28
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-10-28
Total releases: 5 / 4 yrs
License: Apache License (>= 2)
Minimum R: ≥ 3.5.0
Bundled data: 1.6 MB / 9 files
Download size: 1.7 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("metevalue")

Format

Yang, Y., Liu, H., & Pan, X. (2023). metevalue: E-Value in the Omics Data Association Studies (Version 0.2.4) [Computer software]. https://doi.org/10.32614/CRAN.package.metevalue

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 metevalue version 0.2.4 [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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