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refseqR: an R package for common computational operations with records on RefSeq collection.

¹Department of Genetics-ETSIAM, University of Cordoba, Córdoba, 14071, Spain.

Bioinformatics Advances

|September 3, 2024

Summary

We developed refseqR, an R package for easy computational analysis of National Center for Biotechnology Information (NCBI) RefSeq entries. This tool enhances data integration with Bioconductor objects for broader applications.

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Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Accessing and processing data from the National Center for Biotechnology Information (NCBI) RefSeq database is crucial for biological research.
Existing tools may lack user-friendliness or specific functionalities for RefSeq record manipulation.

Purpose of the Study:

To introduce refseqR, a novel R package designed for streamlined computational operations on RefSeq entries.
To provide a user-friendly interface for interacting with curated records from the RefSeq database.
To facilitate interoperability with existing Bioconductor objects for enhanced data analysis workflows.

Main Methods:

Development of an R package named refseqR.
Implementation of functions for common computational tasks on RefSeq entries.
Ensuring compatibility and integration with Bioconductor infrastructure.

Main Results:

refseqR offers a user-friendly solution for handling RefSeq data.
The package enables efficient computational operations on GenBank and NCBI records.
Interoperability with Bioconductor objects is a key feature, allowing integration into diverse projects.

Conclusions:

refseqR simplifies the analysis of RefSeq database entries.
The package enhances the utility of biological data by enabling seamless integration with other bioinformatics tools.
refseqR is available as an open-source R package on CRAN.