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Computing enrichments, similarities, and counts ...

Many features in CoNekT rely on pre-populating tables with data. This allows search functions to quickly filter on certain terms.

Computing Counts

After building or extending a database updating counts is crucial for several features to work. In 'Build' click on 'Update Counts' to start this process.

update_counts

Other things to pre-calculate are :

Clade Assignments : 'Build'->'Assign Clades' GO summaries for families : 'Build'->'Family-wise annotation' Reconsiliated Tree : 'Build'->'Reconsile Trees' Expression Context Conservation (ECC) : 'Build'->'Expression Context Conservation (ECC)'

Similarities between co-expression clusters : 'Build'->'Cluster Similarities' GO Enrichment for co-expression clusters : 'Build'->'Cluster GO Enrichment' Predict GO labels from the network : 'Build'->'Predict GO from Neighborhood'

Note that if any of these are missing the corresponding features in the DB will simply be disabled.

Finally there is one Experimental feature that turns neighborhoods into clusters. while this enables GO-enrichment for neighborhoods, it messes up cluster similarities. This can be useful in case no network clustering is performed. 'Build' -> 'Neighborhood to clusters'