RFoldali

RFoldali is a software tool designed for the analysis of RNA-Seq data, specifically focusing on the identification of differentially expressed genes and the visualization of gene expression patterns. Developed by the Bioinformatics and Computational Biology Group at the University of California, San Diego, RFoldali leverages the R programming language and its extensive ecosystem of statistical and graphical tools.

The primary function of RFoldali is to perform differential expression analysis on RNA-Seq data. It takes as input raw RNA-Seq read counts and metadata, and outputs a list of genes that are significantly differentially expressed between different experimental conditions. The tool employs statistical methods such as the negative binomial distribution and empirical Bayes moderation to account for the high variability and low counts characteristic of RNA-Seq data.

In addition to differential expression analysis, RFoldali provides functionalities for data normalization, quality control, and visualization. It can generate various plots, including MA plots, volcano plots, and heatmaps, to help researchers interpret their results and identify biologically relevant patterns.

RFoldali is open-source and freely available, making it accessible to researchers with varying levels of bioinformatics expertise. The tool is regularly updated to incorporate the latest advancements in RNA-Seq analysis and to ensure compatibility with new data formats and sequencing technologies.