CHANGES IN VERSION 1.23.1 * Introduced GESECA method for multi-conditional gene set enrichment (see geseca-tutorial vignette for details) * Enrichment table plots now use cowplot (issue #101) * Enrichment table plots are more easily fine-tuned (issue #29) CHANGES IN VERSION 1.21.1 * fix a reproducibility problem (https://github.com/ctlab/fgsea/issues/110) CHANGES IN VERSION 1.19.4 * plotGseaTable now accepts units vector for column widths CHANGES IN VERSION 1.19.2 * Fixed fora() failing to run on a single pathway * Fixed problems random gene set generation for large k (issue #94) * Changed default eps to 1e-50 CHANGES IN VERSION 1.15.2 * Faster perturbate thanks to Nikolay Budin * Cleaner P-value and error estimations CHANGES IN VERSION 1.13.4 * mapIdsList for faster conversion of leadingEdges * experimental support of hypergeometric tests with fora() and collapsePathwaysORA() CHANGES IN VERSION 1.13.3 * experimental support for one-tailed tests CHANGES IN VERSION 1.13.2 * fgsea() implementation changed from simple to multilevel algorithm * proper handling of duplicate genes in gene sets for fgseaSimple() and fgseaMultilevel() CHANGES IN VERSION 1.11.2 * Simpler handling of conditional probabilities * Added the exact algorithm to inst folder CHANGES IN VERSION 1.11.1 * Proper absEps handling CHANGES IN VERSION 1.9.6 * Fix in log2err calculation CHANGES IN VERSION 1.9.6 * Small fixes for plotGseaTable CHANGES IN VERSION 1.9.2 * Added fgseaMultilevel function for more accurate logPval estimation CHANGES IN VERSION 1.7.1 * Setting colwidth to zero make column not to be drawn * Changable line width in plotEnrichment CHANGES IN VERSION 1.5.2 * fgsea throws warning for rank ties * fgsea throws warning for duplicate gene names * Leading edge is now ordered by decreasing of absolute statistic value CHANGES IN VERSION 1.5.1 * Reproducibility fixes * Added collapsePathway function to intelligently collapse overlapping pathways * Added fgseaLabel function for label-permuting GSEA CHANGES IN VERSION 1.1.2 * Fixed building issues CHANGES IN VERSION 1.1.1 * Fixed bug: not using Multicore on Windows CHANGES IN VERSION 0.99.8 * Results are now reproducible with set.seed() CHANGES IN VERSION 0.99.7 * Performance improvement: slightly better sampling and better segment tree CHANGES IN VERSION 0.99.6 ------------------------- * Fixed bug with failing when zero pathways are analyzed CHANGES IN VERSION 0.99.5 ------------------------- * Using `BiocParallel` package instead of `parallel` * Implemented leading edge analysis (`leadingEdge` column of fgsea result)