CHANGES IN VERSION 1.1.7
-----------------------

NEW FEATURES

    o Populate annotations

    o Fix bugs
    
    o Modify the function 'xSubneterGenes' with threshold output

    o Add functions ('xSubneterGenesAdv' and 'xSubneterGenesMST') supporting multiple subnetwork identifications

    o Modify the functions ('xSubneterGR' and 'xSubneterSNP') enabling multiple subnetwork identifications
    
    o Modify the function 'xLayout' with new layouts (dephi and graphlayouts)
    
    o Modify the function 'xRDataLoader' supporting buit-in datasets hosted at OSF
    
    o Add a function ('xMarkNet') supporting network marking
    

CHANGES IN VERSION 1.1.6
-----------------------

NEW FEATURES

    o Fix bugs
    
    o Simplify functionalities
    

CHANGES IN VERSION 1.1.5
-----------------------

NEW FEATURES

    o Populate annotations
    
    o Add functions ('xEnrichRadial', 'xEnrichDotplot', 'xEnrichChord', 'xEnrichD3', 'xEnrichCtree', 'xCtree', 'xEnrichGGraph', 'xGGraph') for radial-, dot-, chord-, D3 and tree-style plot of enrichment results

    o Add functions ('xWCN' and 'xWCNheatmap') for weighted correlation network analysis
    
    o Add a new function 'xLayout' for adding graph node coordinates into a graph

    o Add a new function 'xObjSize' for estimating the memory allocation

    o Modify functions ('xSymbol2GeneID', 'xGeneID2Symbol', 'xDefineOntology', 'xEnricherGenes') enabling organism-specific customised analysis
    
    o Add functions ('xGraphRWR', 'xGraphSim', 'xGraphPerf') for analysing graph node similarity
    
    o Add functions ('xGraphML2AA') for pathway analysis

    o Add functions ('xPieplot') for pie plot
    
    o Add functions ('xAge') for Phylostratigraphy analysis

    o Unify auxiliary functions ('xAuxFunArgs', 'xAuxRd2HTML', 'xAuxRdWrap' and 'xAuxEmbed')

    o Add a new function 'xReport' enabling dynamic reports
    
    o Add new functions ('xME', 'xMEplot', 'xMEbesd', 'xMEsmr', and 'xMEabf') enabling eQTL and its downstream analysis
    

CHANGES IN VERSION 1.1.4
-----------------------

NEW FEATURES

    o Populate annotations

    o Add function 'xRPS' for calculating regulatory potential scores
    
    o Add functions ('xGRmanhattan' and 'xGRkaryogram') for genomic region manhattan and karyogram plot

    o Add functions ('xLDblock', 'xLDsampling' and 'xLDenricher') for LD block operations

    o Add functions ('xDefineOntology', 'xDefineGenomicAnno', 'xDefineEQTL' and 'xDefineHIC') for defining ontology and its annotations, genomic annotations, eQTL and promoter capture Hi-C datasets

    o Add function 'xPCHiCplot' for visualising promoter capture Hi-C datasets

    o Add function 'xBiproject' for bigraph projection
    
    o Add functions ('xRWenricher' and 'xRWkernel') for network enrichment analysis

    o Add function 'xRepurpose' for drug repurposing
    

CHANGES IN VERSION 1.1.3
-----------------------

NEW FEATURES

    o Populate annotations
    
    o Fix bugs in the function 'xGRviaGenomicAnno' (disabling OR calculation)
    
    o Add function 'xEnrichHeatmap' for visualising enrichment results in a heatmap
    
    o Add functions ('xGRoverlap' and 'xGRtrack') enabling extraction and analysis of genomic scores
    

CHANGES IN VERSION 1.1.2
-----------------------

NEW FEATURES

    o Populate annotations
    
    o Fix bugs in the functions 'xEnrichConciser' and 'xEnrichForest'

    o Modify functions ('xEnricher', 'xEnricherGenes', 'xEnricherSNPs', 'xEnricherYours', 'xEnricherGenesAdv', 'xGRviaGeneAnno' and 'xGRviaGeneAnnoAdv') enabling the control of, adding 'background.annotatable.only', how to use the test background 

    o Add functions ('xGR2xGeneAnno' and 'xGR2xGeneAnnoAdv') supporting genomic region-based enrichment analysis using the crosslinked gene annotations
    
    o Add a new function 'xEnrichTreemap' for visualising enrichment results in a treemap
    
    o Add a new function 'xCrosstalk' for active pathway crosstalk identification
    
    o Add new functions ('xGRsort', 'xGRsep' and 'xGRcse') for genomic range operations

    o Add a new function 'xEnrichLadder' for ladder-like plot of enrichment results


CHANGES IN VERSION 1.1.1
-----------------------

NEW FEATURES

    o Modify functions ('xEnricher', 'xEnricherGenes', 'xEnricherSNPs', 'xEnricherYours', 'xGRviaGenomicAnno') enabling two-side p-value calculation and inclusion of odds ratio (confidence intervals)

    o Add a new function 'xEnricherGenesAdv' for conducting enrichment analysis given a list of gene sets and a list of ontologies
    
    o Add a new function 'xGRviaGeneAnnoAdv' for conducting enrichment analysis given a list of genomic region sets and a list of ontologies
    
    o Add a new function 'xEnrichForest' for visualising enrichment results in a forest plot

    o Add a new function 'xVisInterpAnimate' for animating irregular data interpolation and visualisation
    
    o Modify 'xDAGpropagate' allowing for keeping all children
    
    o Modify 'xSNP2nGenes' and 'xSNP2GeneScores' allowing for inclusion of a TAD dataset to pre-filter SNP-nGene pairs
    
    o Modify 'xEnrichBarplot', 'xEnrichCompare', 'xVisNet', 'xVisInterp', 'xVisInterpAnimate' and 'xVisEvidence' allowing for inclusion of font family
    
    o Populate the primary source KEGG into 'xEnricherGenes', 'xGRviaGeneAnno', 'xDefineNet', 'xSubneterGenes', 'xSubneterSNPs' and 'xSubneterGR'
    
    o Add a new function 'xCombineNet' for combining networks

    o Modify 'xGR2nGenes' allowing for user-defined 'GR.Gene' (a GR object)
    
    o Modify 'xEnrichDAGplot' only visualising nodes within a user-defined graph (an igraph object)
    
    o Populate annotations (KEGG and REACTOME)

    o Add a new function 'xGraphML' for creating a graphml file

    o Add a new function 'xVolcano' for drawing a volcano plot

    o Add a new function 'xAddCoords' for adding coordinates into a graph by a node attribute

    o Add a new function 'xGraphSplit' for splitting a graph by a node attribute
    
    o Add a new function 'xRegress' for regressing out data by principle components
    
    o Add functions ('xGGnetwork' and 'xOBOcode') enabling ggplot-like visualisation
    
    o Add functions ('xGScore' and 'xGScoreAdv') enabling extraction of genomic scores  

    o Add functions ('xBigraph' and 'xBiheatmap') supporting bigraph analysis

    o Add functions ('xGR2xGenes', 'xGR2xGeneScores' and 'xGR2xNet') supporing genomic region analysis using the crosslink info
    
	
CHANGES IN VERSION 1.0.10
-----------------------

NEW FEATURES

    o Add a new function 'xVisInterp' for irregular data interpolation and visualisation
    
    o Populate annotations

    o Modify 'xSymbol2GeneID' allowing for converting into gene info
        
    o Define S3 classes ('eTerm')

    o Add a new function 'xDefineNet' for defining built-in network
    
    
CHANGES IN VERSION 1.0.9
-----------------------

NEW FEATURES

    o Add a new function 'xSymbol2GeneID' for converting gene symbols to entrez geneid
    
    o Add a new function 'xDAGpropagate' for propagating annotations
    
    
CHANGES IN VERSION 1.0.8
-----------------------

NEW FEATURES

    o Add a new function 'xCheckParallel' for checking and using parallel computing on Unix-like systems and on Windows
    
    o Enable parallel computing on Windows ('xDAGsim', 'xSocialiser' and 'xGRviaGenomicAnnoAdv')
    
    o Populate annotations
    

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

NEW FEATURES

    o Fix bugs (such as in 'xGRviaGeneAnno', 'xGRviaGenomicAnno' and 'xGRviaGenomicAnnoAdv')
    
    o Get published in Genome Medicine (see http://dx.doi.org/10.1186/s13073-016-0384-y)
    

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

NEW FEATURES

    o Change functions ('xEnrichBarplot' and 'xEnrichCompare') caused by the major ggplot2 update (2.2.0)
    
    o Add a new function 'xColormap' for defining color palette (including those used by ggplot2)

    o Add new functions ('xSubneterGR', 'xGR2GeneScores', 'xGR2nGenes' and 'xGRscores') to conduct region-based network analysis
    
    o Populate annotations
    

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

NEW FEATURES

    o Add infrastructure functions ('xSNPlocations' and 'xSM2DF')

    o Populate annotations


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

NEW FEATURES

    o Fix bugs in the function 'xRDataLoader' for Windows users
    
    o Enable choosing analysis resolution done by 'xGRviaGenomicAnno'
    
    
CHANGES IN VERSION 1.0.2
-----------------------

NEW FEATURES

    o Add new functions ('xEnrichConciser', 'xEnrichBarplot', 'xEnrichDAGplot', 'xEnrichCompare' and 'xEnrichDAGplotAdv') to visualise and compare enrichment analysis results
    
    o Add new functions ('xSocialiserDAGplot' and 'xSocialiserDAGplotAdv') to visualise and compare similarity analysis results
    
    o Add new functions ('xVisKernels', 'xSNPscores', 'xSNP2nGenes', 'xSparseMatrix' and 'xSNP2GeneScores') to control how to define and score seed genes from a list of GWAS SNPs
    
    o Add new annotation functions ('xGRviaGeneAnno', 'xGRviaGenomicAnno' and 'xGRviaGenomicAnnoAdv') to interpret user-defined list of genomic regions either via looking at nearby gene annotations by ontologies or via looking at co-localised functional genomic annotations


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

NEW FEATURES

    o A new data interpretation system by comprehensively utilising ontology and network information to make a user-defined gene or SNP list more interpretable

    o Enrichment analysis using either built-in or custom ontologies

    o Similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles
    
    o Network analysis for identifying gene networks given a query list of (significant) genes or SNPs
    