XPathway

XPathway

XPathway, a set of  tools that compares pathway activity analyzing mapping of contigs assembled from RNA-Seq reads to KEGG pathways. The XPathway analysis of pathway activity is based on expectation maximization and topological properties of pathway graphs.

The different tools that constitute XPathway are:

1.  KGMLPathway2Graph: Extraction tool of metabolic network 

KGMLPathway2Graph aims at extracting metabolic pathways from KGML flatfile database. Readme, examples and software for KGMLPathway2Graph can be downloaded here .

2. Link Gopher 1.3.3:  Mozilla Firefox add-ons

• open kegg result page “pathway map”
• use this filter “http://www.kegg.jp/kegg-bin/show_pathway?@” with link gopher to copy all green nodes per pathway. These are part of the pathway urls. Save the output in a file.

3. java code: To extract all green nodes 

The code can be downloaded here along with Readme and examples.

4. Python code: To compute pathway activity level and significance. 

The code can be downloaded here here along with Readme and examples.

5. shell script: To download all KGML file from Kegg using wget. This is a one time operation since ko xml file do not change. Code is available   here

Infer Pathway activity level pipeline and Pathway significance pipeline

Use the steps provided in the Readme  here Activity_level_and_Significance_Pipeline.