CoNet

CoNet is a Cytoscape plugin that detects significant associations in presence/absence and abundance matrices.
CoNet 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). Features - 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 (also implemented in R package 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

1.1.1.beta

Works with Cytoscape 3.0

Release Notes

1.1.1.beta (26th May 2016) -------------------------- - improved lineage treatment - fixed higher-level taxon assignment in the presence of groups - fixed feature sample matching when biom HDF5 file is provided - CoNet can now load adjacency matrices as networks (allows loading SparCC results)

1.1.0.beta

Works with Cytoscape 3.0

Release Notes

1.1.0.beta (27th January 2016) ---------------------------- - CoNet compiled for Cytoscape 3.X now requires at least Java 7 (previously Java 6), Java 6 compatibility is maintained for CoNet compiled for Cytoscape 2.X - CoNet compiled for Cytoscape 3.X can now load biom HDF5 files directly using the BiomIO class by Joshua Ladau - improved handling of missing lineages and lineages with non-unique names - fix of an irregular bug due to a problem in thread handling in the speed-up part of CoNet

1.0.7.beta

Works with Cytoscape 3.0

Release Notes

1.0b7 (29th June 2015) ----------------------- - improved table parsing (error messages specify problems better) - apriori wrapper adjusted to latest version of apriori (6.12), previous apriori versions will no longer work - bug fix for combining apriori with multiple-testing correction (previously, error message prevented this) - fixed error when combining groups with feature file - row groups can now be combined with higher-level taxon assignment - new help system introduced, fixing the help display problems that occurred previously on some systems - matrix property display problem for incidence matrices fixed - removal of all-zero taxa after down-sampling of samples and all-zero samples after down-sampling of taxa - fixed initial edge selection parameter disappearance after export to settings file or cmd line call generation fixed

1.0.6.beta

Works with Cytoscape 3.0

Release Notes

1.0b6 (19th August 2014) ------------------------ - change of license (from 22nd May 2014 onwards, CoNet is distributed under the GNU General Public License version 2) - fixed bug in Kendall implementation - treatment of ties in Spearman implementation fixed - fixed problem of setting initial edge selection parameter from settings file - if groups are provided, the group properties are listed when matrix info is selected - improved taxonomy parsing from biom files (hit number is parsed if provided) - fixed rarefaction bug (previously, error message prevented to carry out rarefaction) - network comment does no longer list removed edges and filtered rows, to reduce size of big networks - logging level can now be adjusted (defaults to fatal to reduce size of log file) **WARNING:** A serious bug was spotted in Jean-Sebastien Lerat's Spearman implementation, which occurred when missing value treatment was set to pairwise_omit. This bug is now fixed, but networks constructed with Spearman and missing value treatment enabled need to be reconstructed.

1.0.5.beta

Works with Cytoscape 3.0

Release Notes

1.0b5 (15th April 2014) ----------------------- - added p-value computation with Fisher's Z-score for correlations - Lallich routine selection without multiple test correction rejected - bug fixed - parsing error for sample names starting with E/e and followed by numeric value fixed - fixed positive-edges-only filter - fixed computation of maximum number of zeros per row (for matrix property display) - added error message in case automatically obtained lower and upper threshold overlap

1.0.4.beta

Works with Cytoscape 3.0

Release Notes

1.0b4 (20th December 2013) -------------------------- - implemented export of positive and negative node degree - option added to report input matrix properties and suggestion of CoNet settings based on these properties - fixed settings file bug (disable speedup not set/exported from/to settings file) - fixed settings file bug (minzeropairs filter not set from settings file) - fixed settings file bug (copresence/mutual exclusion-only-filter not set back correctly to default) - fixed command line export bug (--topbottom not exported) - fixed treatment of feature rows for taxa without lineages in renormalization - edges for which methods infer conflicting interaction types are filtered now - row combination involving summed row are forbidden now

1.0.3.beta1

Works with Cytoscape 3.0

Release Notes

1.0b3.1 (28th October 2013) ---------------------------- - Jean-Sebastien Lerat's library KLD implementation: removed division by number of value pairs - bug fix for networks merged on the score level - improved non-SGE parallelization support

1.0.3.beta

Works with Cytoscape 3.0

Release Notes

1.0b3 (22nd October 2013) -------------------------- - fixed bug concerning automatic lineage assignment for higher-level taxa with groups - allow transposing feature matrix - allow feature/input matrix sample matching to support feature data with samples that have a different order than input matrix samples - more flexible OTU table from biom file parsing (support parsing lineages from row names) - better matrix parsing error catching - too large data menu size fixed - prevent generation of command line call in the presence of input errors - removed faulty error message about combining ARACNE with missing values when JSL MI was selected

1.0.2.beta

Works with Cytoscape 3.0

Release Notes

1.0b2 (12th October 2013) ------------------------- - support for MI and Jensen-Shannon with Jean-Sebastien Lerat's library - interface offers 3 MI implementations: minet, aracne and Jean-Sebastien Lerat's library - fixed bug related to keeping discarded rows as one row per group - fixed bug concerning group exclusion (betweengroupsonly, withingroupsonly) - prevent kept summed rows to appear in the network

1.0.1.beta1

Works with Cytoscape 3.0

Release Notes

1.0b1.1 (14th September 2013) ---------------------------------------- - No Blast hit entry supported in QIIME OTU tables - execution of R batch scripts in given directory 1.0b1 (10th September 2013) --------------------------------- CoNet beta release. This release features the re-implementation of the CoNet core by Jean-Sebastien Lerat. The re-implementation included the renormalization and the measures: - Pearson - Spearman - Kendall - Hellinger - Euclid - Steinhaus - Bray Curtis - Kullback-Leibler - Variance of Log-ratios - Hilbert-Schmidt independence criterion All measures were tested to give the same networks from test data as the previous implementations. This release also adds the following features: - support of QIIME OTU tables with and without taxonomy - versioning via CoNet property file, valid for both Cytoscape plugin and command line version - added the possibility to filter rows with less than the given number of non-double-zero pairs - directory of R batch scripts can be specified on command line 0.9 (30th May 2012) -------------------- CoNet alpha release.

CYTOSCAPE 3

Version 1.1.1.beta

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Released 26 May 2016

Works with Cytoscape 3.0

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CYTOSCAPE 2

Version 1.1.1-beta

Released 16 May 2016

Works with Cytoscape 2.7,2.8

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