Pathway Analysis Software

The table below provides a list of freely-available pathway analysis tools chosen by MSI experts.  Our preferred recommendation is the MSI-developed clusterProfilerWrapper, although we have compiled a list of other alternatives that may better suit your needs depending on your project. Please note that with the exception of the clusterProfilerWrapper, these tools are not maintained by MSI.  

Footnotes and abbreviations are explained below the table.

If you would like to see examples of the types of plots created by these tools, please view the gallery link below

IPA Alternatives Gallery


 

Alternative methods
Tool Name GUI/CLI Options Scripting Language Install Link Help Species(*) Prot/Metab Method Extra Functions Notes

clusterProfilerWrapper

R

Pathway Analysis Github

HM+

ORA

[1]

clusterProfiler

  • CLI

R

clusterProfiler Documentation

HM++

ORA + GSEA + Bio Theme Comparison

N/A

Causal Inference Engine

  • Web GUI
  • CLI

R

Causal Inference Engine Documentation

H+

ORA + GSEA

Upstream regulator inference

[2]

ChEA3

  • Web GUI
  • CLI

R

ChEA3 Documentation

HM

ORA

Upstream regulator inference

iDEP

  • Web GUI
  • CLI

R

iDEP Documentation

HM++

ORA + GSEA

[3]

Pathview

  • Web GUI
  • CLI

R

Bioconductor Pathway Package page

HM++

GAGE + ORA

[4]

g:Profiler

  • Web GUI
  • CLI

R/Python

g:Profiler help for APIs, g:Profiler help for R

HM++

ORA

KEGGprofile

  • Web GUI
  • CLI

R

HM

Protein

ORA

modEnrichr

  • Web GUI

Enrichr Help Center

HM+

ORA

[5]

ShinyGO

  • Web GUI

ShinyGO Documentation

HM++

ORA

Promoter motif enrichment

Reactome

  • Web GUI

Reactome User Guilde, Reactome YouTube

HM+

Both

ORA

ToppGene

  • Web GUI

ToppGene Suite documentation

HM

Protein

Proprietary

Pharmacome annotations

GSEA

  • Standalone GUI
  • Web GUI
  • CLI

NA

GSEA Main Page

H

GSEA

[4]

Galaxy

  • Standalone GUI
  • Web GUI

Galaxy Training Page

HM

GSEA

iGEAK

  • Standalone GUI

iGEAK! User Manual

HM

ORA + GSEA

[6]

Cytoscape

  • Standalone GUI

Cytoscape User Manual

N/A

N/A

Visualization

[7]

Blast2GO

  • Standalone GUI

ORA + GSEA

Functional annotation

[8]

Most tools can:
1) Handle methylation data if you use probes with associated genes, though most will not correct for bias.
2) Handle other species IF you are willing to make assumptions about orthology and conservation of pathways!

Notes:
1. End-to-end analysis. Expression counts -> DE testing -> enrichment
2. Free registration required. In the case of GSEA, GenePattern also requires registration
3. Registration possible - allows more features (largely just saving data)
4. Not tested (and apparently not working) on latest MacOS versions!
5. Primarily a visualization tool. But has lots of plug-ins/apps for both analysis and visualization.
6. Can handle more species via commandline tool
7. Can functionally annotate genes (from non model organisms)

Species(*):
HM  - Human, Mouse
HM+ - Human, Mouse, other model organisms
HM++ - Human, Mouse, other ensembl species