Resources : HeatmapGenerator

Applications

One use case for the HeatmapGenerator pertains to RNA next-generation sequencing data (RNAseq). The main goal of RNAseq is to quantify gene expression across multiple biological samples. However, there is no gold standard analysis pipeline for RNAseq data. Rather, there are multiple forms of pipelines that look at the same data, but in two different ways. First, there is a very simplistic model of generating raw counts. These raw counts are generated after global alignments by a program such as HTseq. Second, there is an alternative mathematical approach to calculate a normalized value in order to scale the expression of each gene relative to its respective size (in base pairs). This method is performed by Cufflinks, which outputs the normalized value called fragments per kilobase per million (FPKM). The HeatmapGenerator software program is built to handle both types of data. The user can enter in either raw counts per gene or FPKM per gene, and the HeatmapGenerator will show the differential expression analyses in a visual manner.