geneNR

3.0.0

Automated Gene Identification for Post-GWAS and QTL Analysis

0packages depend

2.1Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Rajamani NirmalarubanFirst published 2025-03-103 releasesCRAN page ↗

Facilitates the post-Genome Wide Association Studies (GWAS) and Quantitative Trait Loci (QTL) analysis of identifying candidate genes within user-defined search window, based on the identified Single Nucleotide Polymorphisms (SNPs) as given by Mazumder AK (2024) doi:10.1038/s41598-024-66903-3. It supports candidate gene analysis for wheat and rice. Just import your GWAS result as explained in the sample_data file and the function does all the manual search and retrieve candidate genes for you, while exporting the results into ready-to-use output.

Install

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

install.packages("geneNR", 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-genenr

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-geneNR

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-geneNR

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

Health

CRAN checks

1NOTE12OK

Failing flavors

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

Slowest check: 1.3 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 57%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.1K

CRAN downloads in the past year

Rank #20,462 · ~6/day · ~178/mo

Releases R versions

Daily download trend is not available in this view yet.

18030 days

54690 days

2.1K1 year

Compare downloads with other packages →

Also on90 r2u

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (10)

readr stringrutilshttr rvest xml2 writexl vcfR ggplot2 ggrepel

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown devtools

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (12)

Maintainer (1)

Rajamani Nirmalaruban

Author, Maintainer, Copyright holder

Authors (12)

Rajamani Nirmalaruban

Author, Maintainer, Copyright holder

Author

Author

Author

Author

Author

Author

Author · added in 3.0.0

Author

Author

Author

Author

Rajamani Nirmalaruban

Author, Maintainer, Copyright holder

Package Timeline

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

3.0.0Latest
2026-07-05 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
2.0.1
2025-03-29 · diff ↗
1.0.1
2025-03-10
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-03-10
Total releases: 3 / 1 yrs
License: CC BY 4.0
Minimum R: ≥ 3.5
Bundled data: 1.6 KB / 5 files
Download size: 65 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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