RNAfager

RNAfager is a bioinformatics software package designed to process, annotate, and visualize RNA sequencing (RNA-seq) data. It combines standard preprocessing routines with modular analysis components to support transcript quantification, differential expression testing, and transcript assembly in a single workflow.

The software accepts common sequencing inputs such as FASTQ and aligned BAM files and produces outputs including quality-control reports, count matrices, normalized expression values, and annotated transcript models. Core features typically include adapter trimming, read alignment or pseudoalignment, transcript-level quantification, and integration with downstream statistical tools for differential expression and functional enrichment.

RNAfager is built with extensibility in mind, providing a plugin architecture or workflow engine that allows users to add new tools, custom scripts, or alternative aligners. It commonly offers both a command-line interface for batch processing and a graphical or web-based interface for exploratory analysis and visualization of expression patterns, PCA, and clustering results.

Typical use cases include bulk RNA-seq analysis, exploratory transcriptome profiling, annotation of novel isoforms, and preparatory processing for single-cell or long-read RNA workflows. The software is often packaged under a permissive open-source license and developed collaboratively by bioinformatics groups, enabling community contributions and reproducible pipelines.

Documentation and user guides usually cover installation, input formatting, recommended parameter settings, and examples of common analysis scenarios. Community feedback and benchmarking against established pipelines are used to inform improvements and validate performance across different experimental designs.