Metadata-Version: 1.2
Name: struct-lmm
Version: 0.1.1
Summary: Linear mixed model to study multivariate genotype-environment interactions
Home-page: https://github.com/limix/struct-lmm
Maintainer: StructLMM developers
Maintainer-email: casale@ebi.ac.uk
License: Apache License 2.0'
Description: # struct-lmm
        
        [![Travis](https://img.shields.io/travis/com/limix/struct-lmm.svg?style=flat-square&label=linux%20%2F%20macos%20build)](https://travis-ci.com/limix/struct-lmm) [![Documentation](https://img.shields.io/readthedocs/struct-lmm.svg?style=flat-square&version=stable)](https://struct-lmm.readthedocs.io/)
        
        Structured Linear Mixed Model (StructLMM) is a computationally efficient method
        to test for and characterize loci that interact with multiple environments.
        
        ## Install
        
        From terminal, it can be installed using [pip](https://pypi.python.org/pypi/pip):
        
        ```bash
        pip install struct-lmm
        ```
        
        ## Getting Started
        
        Interaction with StructLMM happens in the terminal via the following command
        line tools installed with the package, and described at the [Command Line Interface](http://struct-lmm.readthedocs.io/en/latest/commandline.html)
        section of the [documentation](http://struct-lmm.readthedocs.io/):
        
        - norm_env
        - struct_lmm_analyze
        - lmm_int_analyze
        - lmm_analyze
        - struct_lmm_analyze
        
        ## Usage example
        
        StructLMM can be run from the command line using the following
        
        ```bash
        wget http://www.ebi.ac.uk/~casale/data_structlmm.zip
        unzip data_structlmm.zip
        
        BFILE=data_structlmm/chrom22_subsample20_maf0.10
        PFILE=data_structlmm/expr.csv
        EFILE0=data_structlmm/env.txt
        EFILE=data_structlmm/env_norm.txt
        
        norm_env  --in $EFILE0 --out $EFILE
        
        struct_lmm_analyze --bfile $BFILE --pfile $PFILE --pheno_id gene10 --efile $EFILE --ofile out/results.res --idx_start 0 --idx_end 1000 --batch_size 100 --unique_variants
        ```
        
        Further examples can be found at [http://struct-lmm.readthedocs.io/](http://struct-lmm.readthedocs.io/).
        
        ## Documentation
        
        Documentation is available online at
        [http://struct-lmm.readthedocs.io/](http://struct-lmm.readthedocs.io/).
        
        ## Problems
        
        If you encounter any problem, please, consider submitting a [new issue](https://github.com/limix/struct-lmm/issues/new).
        
        ## Authors
        
        - **Rachel Moore** - [https://github.com/rm18](https://github.com/rm18)
        - **Danilo Horta** - [https://github.com/horta](https://github.com/horta)
        - **Francesco Paolo Casale** - [https://github.com/fpcasale](https://github.com/fpcasale)
        
        ## License
        
        This project is licensed under the Apache License (Version 2.0, January 2004) -
        see the [LICENSE](LICENSE) file for details
        
Platform: UNKNOWN
