R Observatory: Metrics for GFFStrandLoc version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GFFStrandLoc

0.1.0

Strand-Wise Gene and Protein Extraction from GFF3 Files

0packages depend

1.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Subham GhoshFirst published 2026-04-151 releasesCRAN page ↗

Facilitates the extraction and organization of strand-specific genomic features from GFF3 files. In many species and variants, high quality genome annotations are not always available, necessitating de novo annotation using tools such as AUGUSTUS (Stanke et al., 2006; doi:10.1093/nar/gkl200). However, downstream processing of such annotations to obtain structured information, such as strand-wise gene locations, transcript regions, and associated protein identifiers—can be computationally intensive and complex. 'GFFStrandLoc' provides a streamlined framework to parse GFF3 files and generate structured outputs containing strand-wise and region-wise genomic coordinates for each transcript, along with their associated protein information. Additionally, it enables users to define custom promoter lengths and extract corresponding promoter region coordinates for genes in a strand-aware manner. By simplifying post-annotation processing, it enhances the usability of de novo annotated genomic datasets for downstream analysis and interpretation.

Install

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

install.packages("GFFStrandLoc", 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-gffstrandloc

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-GFFStrandLoc

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-GFFStrandLoc

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

Health

CRAN checks

13OK

Slowest check: 38 s · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

0

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-16
4 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

1.3K

CRAN downloads in the past year

Rank #14,734 · ~3/day · ~104/mo

Releases R versions

Daily download trend is not available in this view yet.

12930 days

70490 days

1.3K1 year

Compare downloads with other packages →

Also on33 r2u14 autocran

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (8)

Maintainer (1)

Subham Ghosh

Author, Maintainer

Authors (8)

Subham Ghosh

Author, Maintainer

UB Angadi

Author

Monendra Grover

Author

Sayanti Guha Majumdar

Author

Author

Author

Author

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-04-15 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-04-15
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Download size: 7.8 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GFFStrandLoc")

Format

Ghosh, S., Angadi, U., Grover, M., Guha Majumdar, S., Mishra, D., Murmu, S., Sinha, D., & Yeasin, M. (2026). GFFStrandLoc: Strand-Wise Gene and Protein Extraction from GFF3 Files (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.GFFStrandLoc

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 GFFStrandLoc version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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