TheCodingCollective / clusterFux

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