Clustering

[iamciera]

At the Plant Biology retreat I talked with many people about clustering methods of RNAseq data. I propose those interested can form a group to discuss clustering options/caveats/resources/tutorials/code on October 29th gathering. We can collectively put together all the resources and code into a common repository during the discussion. Who's in?

[upendrak]

I am in.....

[danfulop]

I'm in too. I'm interested in trying, with any large genomic-scale dataset, a hierarchical DPP clustering method. ...I think it's written for CUDA, but not sure.

[bulksoil]

I'm in. I have count data for specific microbes in different environmental samples based off of 16S rRNA sequencing. I'm looking for meaningful microbe-microbe interactions by clustering into modules. I've done this by correlating the counts of the microbes and clustering into a tree by agglomerative clustering, then pruning the tree. This is very similar to old school gene coexpression analysis, but it seems to work. I'm looking for different ways to do this. I'm also interested for rewriting the dynamicTreeCut package from R into Python.

[rjcmarkelz]

I think that this group name should be cluster_fux. I am in

[vmissirian]

Sounds good to me!

[iamciera]

I made an etherpad so we can collaborate on notes: https://codingcollective.etherpad.mozilla.org/3

I don't think we have time to talk about all the different ways in which we approach clustering, but I thought we could all put down in one space resources that have helped us.