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

gseapy-v0.14.0

🚀 This version further improves the speed of calculation.

New features:

• GSEA, ssGSEA speed up 10x than NumPy implementation (<=0.10.8)
• add read_gmt function to parse gmt file.
• add get_library function to download enrichr library and return a dict
• add enrich function to make over-representation analysis less confusing when using enrichr
• biomart API speedup: bioservices dependency is no longer needed.

Bug fixed

• dotplot, ringplot now supports GSEA results

Full Changelog: v0.13.0...v0.14.0

gseapy-v0.13.0

Fixed a critical bug in NES null distribution calculation in the Rust code. #162

And FDR values is affected in when NES < 0 for gseapy version (0.12.0, 0.12.1).

Please update at least to v0.13.0 to get the correct FDR values.

minor

• improve output files (sort by abs(NES) in descending order)
• generate output gene signature file (gmt) used in the calculation

Full Changelog: v0.12.0...v0.13.0

GSEApy-v0.12.0

This is the first Rust binding of GSEApy

NOTE

This version have bugs in NES calculation
Please update to at lease v0.13.0 to get the correct FDR values!!!

Summary

• This version is re-written in Rust, which solve major problems such a memory cost and speed.
• Rust Binding of GSEApy is at lease 3-fold faster than Numpy implementation and 4 times less memory cost (Prerank module). #134, #142
• New output format are used in this version and will be adpoted in the future releases.
• All API remain the same to the older version of GSEApy(< v0.10.8).

New features:

• Rust binding of GSEApy is much faster than the Numpy version (<=v0.10.8)

• The gene_sets argument in gsea, ssgsea, prerank, now support multiple library inputs, e.g:

  • list: ['KEGG_2016,'KEGG_2021_Human']
  • dict: {'term_1': ['gene1', 'gene2,' ...], ...}
  • multiple libraries seperated by comma: "KEGG_2016,KEGG_2021_Human"
  • single libraries: KEGG_2016
  • or gmt file: "KEGG_2016.gmt"
  • Note: it will save you a lot of time if you put multi-values at once, instead of run each seprately.

• dotplot, heatmap, ringplot improvement quite a lot !

Deprecated

• argument processes are now renamed to threads

gseapy-v0.10.7

• Fix t_test statistics, #141
• Fix a critical bug in phenotype permutation percedure (the permutation for null distribution is accidently not correct for phenotype shuffling proceducre) #140. Please update your results using v0.10.7 (only affects phenotype permutation)
• Add odds ratio output to Enrichr output
• minor docs improvement

gseapy-v0.10.3

Fix Enrichr URL error. #110 , #111

gseapy-v0.10.1

This is a major update.

• Fixed a critical bug in NES calculation #105.
• A few minor improvements for a better and cleaner interactive computing experience
• add a new ranking method: genes with absolute value of signal to noise ( abs_signal_to_noise or abs_s2n)
• change cache directory from ~/.gseapy to ~/.cache/gseapy.

gseapy-v0.9.18

• Drop dependency of bs4
• Performance improvement for large dataset: use joblib instead of multiprocessing #92, #70
• Fixed random seeding. Now FDR results are reproducible #95, #70
• Improve heatmap ticks layout

gseapy-v0.9.13

Bump version