<p>Hi, everyone:</p>

<p>I found that there was no golden standard method for single cell RNA-seq subgroup. There were many papers showed different methods for this analysis. Now I wanna try these different clustering methods to my data. How to evaluate them using R, python, etc. I don&#39;t want to do biological experiments~</p>

<p>Generally, is there a golden standard (methods, books, etc.) for evaluating clustering methods by computer in machine learning area?</p>

<p>Thanks very much !</p>

<p>There is no standard method for evaluating clustering methods other than comparing to some ground truth when it is available. There are however several measures of clustering &quot;quality&quot; e.g. the silhouette (in R <a href="https://stat.ethz.ch/R-manual/R-devel/library/cluster/html/silhouette.html" target="_blank">silhouette</a>). See for example the python <a href="http://scikit-learn.org/stable/modules/clustering.html#clustering-performance-evaluation" target="_blank">sklearn page on evaluating clustering</a>.</p>
