gseapy-v1.1.9

bump version

• fix #309
• bump the version to fix a potential compilation issue that makes results inconsistent between versions #311

Full Changelog: v1.1.8...v1.1.9

gseapy-v1.1.8

Fix the gene names order when call gsea() with permutation_type='gene_set' #308

The affected versions are v1.1.6 and v1.1.7. If you happen to run gseapy.gsea(...., permutation_type='gene_set'), please update and re-run

Full Changelog: v1.1.7...v1.1.8

gseapy-v1.1.7

bump version

1. fix input dataframe format issue. #303, #306,
2. fix linux wheel build #307

Full Changelog: v1.1.6...v1.1.7

gseapy-v1.1.6

What's Changed

• Only check_uppercase for string genes
• Better performance of rust implementation

Full Changelog: v1.1.5...v1.1.6

v1.1.5

What's Changed

• GSEA module
  • output: RES (running enrichment score) error fixed. #299
  • output cls file
  • output rnk file
• new save keyword for func get_library(), now can write GMT file to disk
• better gene_name checking. Lowercase gene symbols will try up case implicitly if most gene symbols are not found in the given gene set

Full Changelog: v1.1.4...v1.1.5

v1.1.4

What's Changed

• fix windows build for python 3.13.
• Add ax keyword to dotplot, barplot
• fix: throw error for empty gene lists in enrich by @quasi-deus in #278
• Update plot.py by @byemaxx in #281

Full Changelog: v1.1.3...v1.1.4

v1.1.3

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

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