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