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 (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

1.0b7 (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

1.0b6 (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.

1.0b5 (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

1.0b4 (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

1.0b3.1 (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

1.0b3 (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

1.0b2 (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

1.0b1.1 (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.