Overview
The heatmap tool creates a heatmap of the gene list and sample selection.

Basic Usage
On page load, a heatmap is created with default settings. There are options to change the distance measure and clustering methods, turn dendrogram/clustering on and off for samples and genes (by default, only genes are clustered).

Example work flow:

1. Add genes to the genelist.
2. Go to exHeatmap to create a heatmap.
3. Select which dimensions to cluster and display dendrogram for:  samples (x-axis) and/or genes (y-axis).
4. Select cluster function and distance methods.

Data
exHeatmap uses TPM (Transcripts Per Kilobase Million) values for absolute expression, and no unit for the relative values. Absolute expression values were generated by aligning RNA-Seq reads to the reference genome and gene annotation with aligned read numbers then used to calculate TPM values.

Implementation
The heatmap tool is implemented in python with the rpy package. The heatmap is created with the R gplots.heatmap2. The website is coded with HTML, PHP and JavaScript.

Standard Score
You can read more about the standard score here.