List of relevant pathway enrichment tools

[kpj]

These tools shall be benchmarked next to ours.

Overview papers:

• https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbz158/5722384
• https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3146-1

[kpj]

PROGENy

• link: https://www.nature.com/articles/s41467-017-02391-6
• main ideas:
  • tba

[kpj]

GSEA

• link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1239896/
• main ideas:
  • classic method

[MartinFXP]

https://academic.oup.com/nar/article/47/22/11563/5614570

• GGMs
• DE
• combines gene expression and chip-seq

[kpj]

Proper table: https://docs.google.com/spreadsheets/d/1WeXNx9j3zfiV2_6TLhwOz0J89DObtZey1bSCFIYF7kc/edit?usp=sharing

[kpj]

Superseded by https://docs.google.com/spreadsheets/d/1WeXNx9j3zfiV2_6TLhwOz0J89DObtZey1bSCFIYF7kc/edit

[kpj]

oh no