Changes in version 1.3-2 (2016-12-22)                  

    o   add ronetGGI to query gene-gene interactions from RONET

    o   officially move geeSetPerm from ribiosGSA to ribiosGSEA

                        Changes in version 1.1-8                        

    o   The GeneSet class and GeneSets class are re-designed to support the concept of 'category', namely classes of gene sets. The old class 'GeneSetsList' is removed because its functionality is represented by GeneSets (which provides even more functionality)

    o   Add FisherResult and FisherResultList objects to support Fisher's exact test based gene set enrichment analysis

    o   readGmt now combines readGmt and readGmts, supporting simultaneous reading of several gmt files

    o   Remove 'geneCountFilter' function and replace with 'filterBySize' S4 generic 

    o   Improved functionality of working with GeneSets

                        Changes in version 1.1-7                        

    o   GSEA file directory changes according to the new server setup

                        Changes in version 1.1-6                        

    o   Clean up importing/depending packages: only methods is depended and other packages are all imported

    o   Add GeneSetsList, a list of GeneSets, to allow simultaneous testing of gene sets in multiple gmt files

    o   Add readGmts

                        Changes in version 1.1-5                        

    o   Add gseaScore and gseaScores function to extract scores from annoGseaRes object(s)

                        Changes in version 1.1-4                        

    o   Add parseGmt function to transform a GMT file into a list of integer indices that is directly applicable for downstream analysis

                        Changes in version 1.1-3                        

    o   Remove mroast2tbl since the latest version of limma is already returning a data.frame

    o   add gmthyper and gmthyperList functions to perform Fisher test with GMT files

    o   clean up gseaES and gseaQvalue functions

                        Changes in version 1.1-2                        

    o   Bug fix in matchGenes and geneCounts.

                        Changes in version 1.1-1                        

    o   parseGSEA functions are added to parse all relevant information from a GSEA output directory

    o   gsName, gsDesc, and gsGenes are harmonized for both GSEA results parsing and general GMT file parsing

    o   Classes and methods are added to handle gene sets and GSEA results

                        Changes in version 1.0-9                        

    o   Variables such as GSEA_GENESET_DIR are exported.

                        Changes in version 1.0-8                        

    o   gseaFingerprint.Rscript does not warn when -sortBy is not specified

                        Changes in version 1.0-7                        

    o   Add list2mat, transforming first-level lists to adjacency matrix

    o   ntpTemplates are updated so that it directly inherits a matrix

                        Changes in version 1.0-6                        

    o   Add function ntp to implement the Nearest Template Prediction Algorithm

    o   Add functions readGmt, gsNames, gsDescs, gsGenes, geneCountFilter, etc. to manipulate GeneSets objects from GMT files

    o   Add ntpTemplates and ntpBiTemplates to construct NTP-templates from GeneSets.

                        Changes in version 1.0-5                        

    o   New feature of gmtIndices: invalid Gene Symbols ("", "-") are removed

                        Changes in version 1.0-4                        

    o   New function added, mroast2tbl, to reformat result lists of limma::mroast into data frame.

    o   New function added, gmtIndices.Rd, to get integer indices of genes in GMT gene set lists from a vector of gene symbols. Used by functions such as 'mroast' and 'camera' in the limma package.

    o   New function added, filterGmtByGeneCount, to filter gmt lists by gene counts.

    o   Improvement of buildGSEAcomm: CHIP_FILE is no longer a mandatory parameter. When the option is missing, the GSEA tool performs no mapping between rnk-file identifiers and GMT-file identifiers, for instance when both files use official gene symbols.

                        Changes in version 1.0-3                        

    o   gseaFingerprint is now able to deal with cases where the phenotypes are now named in default as 'pos' and 'neg'. Since in such cases, the order of positive/negative is not clearly defined, we use the alphabetic order of phenotype names as 'pos' and 'neg'.

                        Changes in version 1.0-2                        

    o   gseaFingerprintMatrix: omit empty directories

    o   gseaFingerprintMatrix: stops if all input directories are detected NOT to be GSEA result folders

    o   gseaQvalue: q-values is given in -log10(p) instead of -log(p) (base-10) to make interpretation easier

    o   Add buildGSEAcomm: build bash commands to run GSEA. Able to deal with irregular file names

                        Changes in version 1.0-1                        

    o   gseaFingerprints.Rscript: remove empty lines from input file

                        Changes in version 1.0-0                        

    o   Establish the ribiosGSEA package

    o   Refactor GSEA-related functions from other packages

    o   Add functions used to extract fingerprints from GSEA results