Z score heat map online tool

Question

[kanwarjag]

I know R can be used for this purpose. I am looking for a free software that can generate a heatmap of z score. The matrix has 300 (columns)X 3000 (Rows). Any suggestion. Thanks

[Kevin Blighe]

R is "free software" and there are many heatmap / clustering packages: Heatmaps in R

To scale your data to Z-scores (by row), you simply need to do:

data.scaled <- t(scale(t(data)))

You should then switch to off further scaling in the heatmap function that you use. When you do this, both the dendrogram(s) and the heatmap will be generated from the Z-scores (some people may prefer to not generate the dendrograms from the Z-scores, but may want their heatmap to display these).

Finally, if you literally just want a heatmap, then you could also just use levelplot(), from lattice package.

[igor]

Are you looking for an R solution or are you looking for an alternative free software that is not R?

[kanwarjag]

Alternative to R that can be used by a non-bioinformatician without any coding knowledge. I tried to use TMV4 but it will not take that large matrix.

[igor]

There are a few different graphical options with examples listed here: https://github.com/igordot/genomics/blob/master/notes/heatmaps.md