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NEWS
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NEWS
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Version 1.3-2 (2016-12-22)
+ add ronetGGI to query gene-gene interactions from RONET
+ officially move geeSetPerm from ribiosGSA to ribiosGSEA
Version 1.1-8 (Aug 18, 2015)
+ 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)
+ Add FisherResult and FisherResultList objects to support Fisher's exact test based gene set enrichment analysis
+ readGmt now combines readGmt and readGmts, supporting simultaneous reading of several gmt files
+ Remove 'geneCountFilter' function and replace with 'filterBySize' S4 generic
+ Improved functionality of working with GeneSets
Version 1.1-7 (Jul 07, 2015)
+ GSEA file directory changes according to the new server setup
Version 1.1-6 (Apr 03, 2015)
+ Clean up importing/depending packages: only methods is depended and other packages are all imported
+ Add GeneSetsList, a list of GeneSets, to allow simultaneous testing of gene sets in multiple gmt files
+ Add readGmts
Version 1.1-5 (Aug 19, 2014)
+ Add gseaScore and gseaScores function to extract scores from annoGseaRes object(s)
Version 1.1-4 (Aug 08, 2014)
+ Add parseGmt function to transform a GMT file into a list of integer indices that is directly applicable for downstream analysis
Version 1.1-3 (Apr 14, 2014)
+ Remove mroast2tbl since the latest version of limma is already returning a data.frame
+ add gmthyper and gmthyperList functions to perform Fisher test with GMT files
+ clean up gseaES and gseaQvalue functions
Version 1.1-2 (Apr 11, 2014)
+ Bug fix in matchGenes and geneCounts.
Version 1.1-1 (Apr 07, 2014)
+ parseGSEA functions are added to parse all relevant information from a GSEA output directory
+ gsName, gsDesc, and gsGenes are harmonized for both GSEA results parsing and general GMT file parsing
+ Classes and methods are added to handle gene sets and GSEA results
Version 1.0-9 (Dec 02, 2013)
+ Variables such as GSEA_GENESET_DIR are exported.
Version 1.0-8 (Jun 28, 2013)
+ gseaFingerprint.Rscript does not warn when -sortBy is not specified
Version 1.0-7 (Feb 27, 2013)
+ Add list2mat, transforming first-level lists to adjacency matrix
+ ntpTemplates are updated so that it directly inherits a matrix
Version 1.0-6 (Feb 26, 2013)
+ Add function ntp to implement the Nearest Template Prediction Algorithm
+ Add functions readGmt, gsNames, gsDescs, gsGenes, geneCountFilter, etc. to manipulate GeneSets objects from GMT files
+ Add ntpTemplates and ntpBiTemplates to construct NTP-templates from GeneSets.
Version 1.0-5 (Nov 19, 2012)
+ New feature of gmtIndices: invalid Gene Symbols ("", "-") are removed
Version 1.0-4 (Nov 01, 2012)
+ New function added, mroast2tbl, to reformat result lists of limma::mroast into data frame.
+ 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.
+ New function added, filterGmtByGeneCount, to filter gmt lists by gene counts.
+ 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.
Version 1.0-3 (Oct 02, 2012)
+ 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'.
Version 1.0-2 (Jul 16, 2012)
+ gseaFingerprintMatrix: omit empty directories
+ gseaFingerprintMatrix: stops if all input directories are detected NOT to be GSEA result folders
+ gseaQvalue: q-values is given in -log10(p) instead of -log(p) (base-10) to make interpretation easier
+ Add buildGSEAcomm: build bash commands to run GSEA. Able to deal with irregular file names
Version 1.0-1 (Jun 07, 2012)
+ gseaFingerprints.Rscript: remove empty lines from input file
Version 1.0-0 (Jun 06, 2012)
+ Establish the ribiosGSEA package
+ Refactor GSEA-related functions from other packages
+ Add functions used to extract fingerprints from GSEA results