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Published August 13, 2022 | Version v0.12.0
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zqfang/GSEApy: GSEApy-v0.12.0

Authors/Creators

  • 1. Harvard Medical School
  • 2. Lamin Labs
  • 3. @NewLimitBio
  • 4. Human Longevity, Inc.

Description

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). #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).
  • 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

Files

zqfang/GSEApy-v0.12.0.zip

Files (5.9 MB)

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Additional details

Related works

Is supplement to
https://github.com/zqfang/GSEApy/tree/v0.12.0 (URL)