Metadata-Version: 1.0
Name: struct-lmm
Version: 0.0.17
Summary: Linear mixed model to study multivariate genotype-environment interactions
Home-page: https://github.com/limix/struct-lmm
Author: StructLMM developers
Author-email: casale@ebi.ac.uk
License: Apache License 2.0'
Description-Content-Type: UNKNOWN
Description: # struct-lmm
        
        Structured Linear Mixed Model (StructLMM) is a computationally efficient method
        to test for and characterize loci that interact with multiple environments.
        
        ## Getting Started
        
        StructLMM is Python package implemented in both Python and R programming
        languages that depends on some libraries implemented in C.
        To make its installation as easy as possible, we make use
        [conda](https://conda.io/), a package manager for software implemented in
        Python, R, and C/C++ (among others) languages.
        
        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
        
        
        ### Requisites
        
        The installation script runs in on GNU/Linux and macOS operating systems.
        It requires either [wget](https://www.gnu.org/software/wget/) or
        [curl](https://curl.haxx.se/) command line tools in case
        [conda](https://conda.io/) is not already installed.
        In any case, the installation script will inform the user if it cannot proceed.
        Otherwise, the StructLMM dependencies is automatically installed and does not
        require user intervention.
        
        ### Install
        
        For Linux and macOS operating systems, struct-lmm can be install from the
        command line by entering
        
        ```bash
        bash <(curl -fsSL https://raw.githubusercontent.com/limix/struct-lmm/master/install)
        ```
        
        The user might be prompted to install conda in case he/she does not have
        it, and will warn the user if for some reason the installation process cannot
        proceed.
        The whole installation process should take less than 15 minutes and mainly
        consists in downloading essential R and Python packages for a working
        environment.
        
        
        ## 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
