CoNet - Co-occurrence Network inference


CoNet - Home

CoNet is a tool that detects significant non-random patterns of co-occurrence (copresence and mutual exclusion) in incidence and abundance data. It has been designed with (microbial) ecological data in mind, but can be applied in general to infer relationships between objects observed in different samples (for example between genes present or absent across organisms). CoNet runs on command line and as a Cytoscape plugin.


new: can parse biom files
support for lagged similarity computation in time series
automatic assignment of higher-level taxa from lineages
large choice of correlation, distance and similarity measures
measures can be combined in multiple ways
implements the ReBoot procedure (published in PLoS Comp Bio), which is also available through ccrepe
significance can be tested with various randomization routines and multiple testing corrections
supports row groups and combination of 2 input matrices
several data preprocessing and filtering options
repeatable data analysis with settings loading and saving
command line tool for the analysis of large data sets