v1.1.2

What's Changed

• Fixed to run prerank without error with rnk (type(pd.Series.name) == str) by @136s in #240
• align gene hits track in TracePlot (fixes #248) by @136s in #249
• Fixed key error in rnk file with duplicated gene names #251

Full Changelog: v1.1.1...v1.1.2

gseapy-v1.1.1

What's Changed

• Corrected odds ratio formula, #237 by @136s in #238

• Refactor internal data parser for files .rnk, .gct. etc

Full Changelog: v1.1.0...v1.1.1

gseapy-1.1.0

What's Changed

New:

• Add gsva module: This is the Rust implementation of GSVA algorithm. #226

Fixed:

• #211, Now, pheno_pos and pheno_neg can define with

from gseapy import GSEA

gs = GSEA(data="./tests/extdata/Leukemia_hgu95av2.trim.txt",
                 gene_sets='KEGG_2016',
                 classes = "./tests/extdata/Leukemia.cls"
)
# set here
gs.pheno_pos = ...
gs.pheno_neg = ...
gs.run()

• improvement for barplot #224. Specify colors for each group explicity

barplot( ....,  color= {'KEGG_2021_Human': 'salmon', 'MSigDB_Hallmark_2020':'darkblue'})

Full Changelog: v1.0.6...v1.1.0

gseapy-v1.0.6

What's Changed

• Fix issue: The gseaplot bar hits aligned incorrectly that happened in v1.0.5, #222
• Add Msigdb API, now mouse symbol/entrze could be download easy, #204, check the docs here
• Add MacOS-Arm64 binary
• A few other minor issues

Full Changelog: v1.0.5...v1.0.6

gseapy-1.0.5

New Features:

• support user-defined background for Enrichr Web Service (on line mode)
• multiple gseaplot. refer to examples. #205
• Enrichr module: add Combined Score output in the local mode

Bug Fixed

• minor issues, #195, #194

Full Changelog: v1.0.4...v1.0.5

v1.0.4

Major:

• Fixed critical bug #190. The wrong output of Lead genes and heatmap are fixed when call gsea with permutation_type = 'gene_set'
  Others
• dotplot visualization improvement
• add new keyword correl_norm_type to ssgsea()

Full Changelog: v1.0.3...v1.0.4

gseapy-1.0.3

Fix issues with

• biomart return status #182
• enrichr gmt output name #181
• logging's log file #180

Full Changelog: v1.0.2...v1.0.3

gseapy-1.0.2

Bump verision

• add more control for dotplot x,y axis order

Full Changelog: v1.0.1...v1.0.2

gseapy-v1.0.1

Minor improvement

• Add enrichment_map function to export GSEApy results to cytoscape, networkx etc. #147
• Refactor DotPlot class to unify dotplot, barplot, enrichment_map.
• Fix dimension when only one significant enriched pathway is left for dotplot, barplot #175
• ringplot has been deprecated. Just use dotplot instead.
• Minor improvements for heatmap.

Full Changelog: v1.0.0...v1.0.1

gseapy-v1.0.0

GSEApy is published in Bioinformatics !

New Features:

• Use Github Actions to build binaries automatically
• Add scRNA-seq tutorial
• Add warnings for duplicated values in the ranking list
• Add Scientific Palettes
• Fix missing ax in barplot ax #171
• Fix other minor issues

Full Changelog: v0.14.0...v1.0.0