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
Tool Name Sort descending | GUI/CLI Options | Scripting Language | Install Link | Help | Species(*) | Prot/Metab | Method | Extra Functions | Notes |
---|---|---|---|---|---|---|---|---|---|
|
HM++ |
ORA |
Promoter motif enrichment |
||||||
|
R |
HM++ |
ORA + GSEA |
[3] |
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|
NA |
H |
GSEA |
[4] |
|||||
|
R/Python |
HM++ |
ORA |
||||||
|
R |
HM++ |
ORA + GSEA + Bio Theme Comparison |
N/A |
|||||
|
R |
HM |
Protein | ORA |
|||||
|
N/A |
N/A |
Visualization |
[7] |
|||||
|
HM |
GSEA |
|||||||
R |
HM+ |
ORA |
[1] |
||||||
|
R |
HM |
ORA |
Upstream regulator inference |
|||||
|
HM+ |
ORA |
[5] |
||||||
|
R |
HM++ |
GAGE + ORA |
[4] |
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|
HM+ |
Both | ORA |
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|
HM |
ORA + GSEA |
[6] |
||||||
|
HM |
Protein | Proprietary |
Pharmacome annotations |
|||||
|
R |
H+ |
ORA + GSEA |
Upstream regulator inference |
[2] |
||||
|
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