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Releases: zqfang/GSEApy

v1.1.3

08 May 18:35
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What's Changed

  • Add Python 3.12 wheels
  • Improve Dotplot usage
  • Update on singlecell example nb to be compatible with missing edges and isolated nodes by @Alireza-Majd in #263

Full Changelog: v1.1.2...v1.1.3

v1.1.2

29 Feb 20:25
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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

21 Dec 22:06
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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

10 Nov 05:30
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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

28 Aug 20:37
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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

15 Jun 22:49
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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

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

v1.0.4

07 Feb 23:51
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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

20 Dec 00:31
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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

13 Dec 00:13
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Bump verision

  • add more control for dotplot x,y axis order

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

gseapy-v1.0.1

08 Dec 20:55
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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