NEWS

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fgsea 1.31.3

• check for empty strings in gene names
• minor fix in leading edge calculation

fgsea 1.31.2

• fora() provides fold enrichment scores for more effective prioritisation of results

fgsea 1.25.1

• introduced plotEnrichmentData() function for more flexible plotting
• update GESECA plot behavior

fgsea 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)

fgsea 1.21.1

• fix a reproducibility problem (https://github.com/ctlab/fgsea/issues/110)

fgsea 1.19.4

• plotGseaTable now accepts units vector for column widths

fgsea 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

fgsea 1.15.2

• Faster perturbate thanks to Nikolay Budin
• Cleaner P-value and error estimations

fgsea 1.13.4

• mapIdsList for faster conversion of leadingEdges
• experimental support of hypergeometric tests with fora() and collapsePathwaysORA()

fgsea 1.13.3

• experimental support for one-tailed tests

fgsea 1.13.2

• fgsea() implementation changed from simple to multilevel algorithm
• proper handling of duplicate genes in gene sets for fgseaSimple() and fgseaMultilevel()

fgsea 1.11.2

• Simpler handling of conditional probabilities
• Added the exact algorithm to inst folder

fgsea 1.11.1

• Proper absEps handling

fgsea 1.9.6

• Fix in log2err calculation
• Small fixes for plotGseaTable

fgsea 1.9.2

• Added fgseaMultilevel function for more accurate logPval estimation

fgsea 1.7.1

• Setting colwidth to zero make column not to be drawn
• Changable line width in plotEnrichment

fgsea 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

fgsea 1.5.1

• Reproducibility fixes
• Added collapsePathway function to intelligently collapse overlapping pathways
• Added fgseaLabel function for label-permuting GSEA

fgsea 1.1.2

• Fixed building issues

fgsea 1.1.1

• Fixed bug: not using Multicore on Windows

fgsea 0.99.8

• Results are now reproducible with set.seed()

fgsea 0.99.7

• Performance improvement: slightly better sampling and better segment tree

fgsea 0.99.6

• Fixed bug with failing when zero pathways are analyzed

fgsea 0.99.5

• Using 'BiocParallel' package instead of 'parallel'
• Implemented leading edge analysis ('leadingEdge' column of fgsea result)