Look into clustering and clustering summarization - Githubissues

sourmash-bio / sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.

http://sourmash.readthedocs.io/en/latest/

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Look into clustering and clustering summarization #225

Open ctb opened 7 years ago

ctb commented 7 years ago

https://stats.stackexchange.com/questions/3685/where-to-cut-a-dendrogram

http://www.sigmath.es.osaka-u.ac.jp/shimo-lab/prog/pvclust/

https://github.com/biocore/genome-subsampler/blob/master/genomesubsampler/prototypeSelection.py

things to provide code for --

notebooks to investigate & viz
include relabling (by editing labels.txt / lists in Python)
cut clusters at some distance (cophenetic?)
bootstrap/summarize/shrink clusters
histogram of distances
selection of samples by fishing with a query (or query set)

ctb commented 7 years ago

@ekg suggested looking into variational autoencoding:

Or, if you're interested in finding your way back into the big tree, you could use VAE or similar dim. > reduction and work from that repr

(we already have t-SNE working in a notebook somewhere)

ctb commented 3 years ago

see cluster and cocluster too #700