Looking for superfast heatmap algorithm
We are planing to develop a gene expression heatmap web visualization, so I am looking for a superfast heatmap algorithm for gene expression data.
- I don't care about the frontend, b/c we are going to develop our own. We are just looking for algorithm that can cluster genes and patients, and generate two dendrograms
- If the number of the genes are huge, we'd like to have a method for automatic gene selection (we can also do z-value visualization; however, z value is dependent on the cohort and thus can not be pre-computed)
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Zhenyu Zhang
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Fastcluster , flexclust
Are you looking for fast drawing of a heatmap or for fast hierarchical clustering or fast drawing of the dendrogram? I'd look at whether R is fast/good enough for your purpose. For fast heatmap generation, you can also look at matrix2png.
Edit: Also for a choice of heatmaps in R, see this post on heatmaps in R.