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.
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.
Are you looking for an R solution or are you looking for an alternative free software that is not R?
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.
There are a few different graphical options with examples listed here: https://github.com/igordot/genomics/blob/master/notes/heatmaps.md
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