CHANGES IN VERSION 1.0.6
-----------------------

NEW FEATURES

    o RData is primarily hosted in https://github.com/hfang-bristol/RDataCentre


CHANGES IN VERSION 1.0.5
-----------------------

NEW FEATURES

    o Add functions 'dcList2Matrix', 'dcAlgoPredictPR', 'dcSupraBetter', 'dcRWRpredict', 'dcNaivePredict'

    o Modify functions 'dcAlgoPropagate' supporting for additively accumulating the score


CHANGES IN VERSION 1.0.4
-----------------------

NEW FEATURES

    o Add functions 'dcFunArgs', 'dcSparseMatrix', 'dcSplitArch', 'dcAlgo', 'dcAlgoPropagate', 'dcAlgoPredict', 'dcAlgoPredictMain' and 'dcAlgoPredictGenome' for creating domain-centric ontology plus their use for predicting ontology terms
    
    o Add databases used for domain-centric ontology term predictions
    
    o Add functions 'dcAncestralML', 'dcAncestralMP' and 'dcDuplicated' for ancestral discrete state reconstruction
    
    o Add functions 'dcSubtreeClade', 'dcSubtreeTips' and 'dcTreeConnectivity' for phylo-formatted tree operations
    

CHANGES IN VERSION 1.0.3
-----------------------

NEW FEATURES

    o Add three functions 'dcBuildInfoDataFrame', 'dcBuildAnno' and 'dcBuildOnto' that are respectively used to build customised objects of S4 classes 'InfoDataFrame', 'Anno' and 'Onto'
    
    o Add an option that allows the user to specify the test background in the function 'dcEnrichment'
    
    o Add annotations of Pfam and InterPro domains and Rfam RNA families by GO, and extend analytical support ('dcEnrichment', 'visEnrichment' and 'dcDAGdomainSim') for these domains/RNAs
    
    o This version is in relation to the publication in PLoS Computational Biology


CHANGES IN VERSION 1.0.2
-----------------------

NEW FEATURES
    
    o Add S4 classes 'Coutput' and 'Cnetwork' to store RWR-based contact outputs and network
    
    o Fix several bugs
    

CHANGES IN VERSION 1.0.1
-----------------------

NEW FEATURES
    
    o Add an S4 class 'Onto' to store ontologies (instead of using 'igraph' previously)
    
    o Add an S4 class 'Eoutput' to store enrichment analysis outputs
    
    o Add an S4 class 'Dnetwork' to store domain networks (eg semantic similarity between domains)
    
    o Add S4 classes 'Coutput' and 'Cnetwork' to store RWR-based contact outputs and network

    o Add the function 'dcConverter' allowing for conversion between classes 'Onto' and 'igraph'


CHANGES IN VERSION 1.0.0
-----------------------

NEW FEATURES

    o Infrastructures for domain-centric ontologies and annotations

    o Domain-based enrichment analysis

    o Semantic similarity between domains according to their annotations by an ontology
    
    o Random Walk with Restart on domain semantic similarity network
    
    o Support for high-performance parallel computing