GSEApy-v0.12.0

[zqfang]

This is the first Rust binding of GSEApy

• 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). Prerank step takes an incredible volume of memory #134, Memory leak #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).
• Please update to v0.11.0 if you have memory or performance issues with GSEApy.

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

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This discussion was created from the release GSEApy-v0.12.0 .