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clusterFux

##Purpose

To understand the intricacies of clustering methods on RNAseq data.

##Method

Analyze the same data set with different clustering methods. Ideally remain inside the R enviroment. Please view/add/edit to wiki for more.

###Clustering

  1. kohonen (Self Organizing Maps) - R, need to pick the # clusters
  2. kmeans() -
  3. hclust() - CUT TREE(consistency between high vs low level analysis, smaller clusters are part of larger ones.
  4. HTScluster - High throughput sequences. server, CPU intensive
  5. WGCNA - hclust() wrapper and ease of use "dynamic tree cut"

###Ordinations

  1. PCA
  2. MDS
  3. PCOA
  4. NMDS
  5. CoCA