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GFFStrandLoc  

Strand-Wise Gene and Protein Extraction from GFF3 Files
View on CRAN: Click here


Download and install GFFStrandLoc package within the R console
Install from CRAN:
install.packages("GFFStrandLoc")

Install from Github:
library("remotes")
install_github("cran/GFFStrandLoc")

Install by package version:
library("remotes")
install_version("GFFStrandLoc", "0.1.0")



Attach the package and use:
library("GFFStrandLoc")
Maintained by
Subham Ghosh
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-04-15
Latest Update: 2026-04-15
Description:
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.
How to cite:
Subham Ghosh (2026). GFFStrandLoc: Strand-Wise Gene and Protein Extraction from GFF3 Files. R package version 0.1.0, https://cran.r-project.org/web/packages/GFFStrandLoc. Accessed 24 Oct. 2026.
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Functions, R codes and Examples using the GFFStrandLoc R package
Full GFFStrandLoc package functions and examples
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