COMPADRE

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WELCOME

COMPADRE is a web - based tool for detection of differentially expressed pathways.
Please enter the following fields to process. Note that all fields are mandatory except for the user geneset and their files.

PROCESS

1. Dataset
2. Class
E.g.: Smoke
3. Database / Geneset GSEA:
Some GMT files were obtained from MSigDB

COMPADRE genesets:
     KEGG Biocarta GOReactome

     User geneset
      (optional)

     Pathway - gene mapping:
     
      Format
      Pathway descriptions:
    
      Format
4. Min genes
Genesets having less than this number of genes .(from dataset) will be ignored
5. Duplicates threshold
Threshold to merge (average) rows. Use 0 to avoid merging.
6. Transformation Log2 Quantile normalization Impute missing data
7. Gene set test
8. Gene set p threshold
9. Gene set q threshold
10. Detection method PCA ICA ISOMAP NMF
11. Components
Suggested value: 1 to 5
12. Component runs
20 Maximum otherwise use R version. Used only for ICA and NMF. Suggested value: 10
13. DEG test
DEG: Differential Expressed Genes
14. DEG p threshold
15. DEG q threshold
16. Permutations
Due to server load, maximum 1,000 permutations are allowed. Please use the R version otherwise.
Exclusive use of SAM test
17. Heatmap color code
18. Heatmap scaling
19. E-mail
Some e-mail clients might detect the e-mail as spam, please revise your junk folder
20. Run


Ave. Eugenio Garza Sada 2501 Sur Col. Tecnológico C.P. 64849 | Monterrey, Nuevo León | Tel. +52 (81) 8358-2000, D.R. Instituto Tecnológico y de Estudios Superiores de Monterrey, México. 2011