PATOWAS: A Pipeline for Analyzing Trait through 'Ome'- wide Association Studies   
Location:  Analysis

Sub-Pipeline 1. Kinship Matrix Calculation
Step 1.1 Upload Quantitative Additive Omics Marker Data (a mxn matrix, e.g Z.csv)   [Download demo]    
- upload data size limit: 2G
 
Sub-Pipeline 2. Trait Analsis Bypass
Step 2.1 Upload Quantative Trait Phenotyic Data (a nx1 vecotr, e.g phe.csv)  [Download demo]    
-upload data size limit:2G
 
Step 2.2 Variance Component Analysis
 
Step 2.3 P-value Scanning for Main Effect Bypass
 
Step 2.4 P-value Scanning for Interaction Effect Bypass


Flowchart of Data Analysis

           

Reminder to the Users:
1. Please carefully check your data file formats before submit: Z matrix files must be comma delimited text .csv file, and stored as m(rows, Bins)xn(cols, Individuals), each row corresponds to one marker(SNP/Gene/Metabolite); phenotype file must be stored as n rows and each row corresponds to one individual.
2. Welcome to contact us(wezhang AT noble.org) for your speicifc data analysis.
3. Please cite our paper: Zhang, W., Dai, X., Xu, S., & Zhao, P. X. (2018). 2D association and integrative omics analysis in rice provides systems biology view in trait analysis. Communications Biology, 1, 153. http://doi.org/10.1038/s42003-018-0159-7.