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apex

Toolkit for QTL mapping and meta-analysis.

APEX is a toolkit for analysis of molecular quantitative trait loci (xQTLs), such as mRNA expression or methylation levels. It performs cis and trans analysis, single- or multiple-variant analysis, and single-study or meta-analysis.

To install APEX from source or download precompiled binaries, see installation guide below.

Analysis modes and documentation

Additional documentation pages

See above for documentation pages on each analysis mode (cis, trans, meta, store). Additional documentation pages are listed below.

Release notes

Installation

APEX is primarily written in C++. To compile APEX from source, run:

git clone https://github.com/corbinq/apex.git
cd apex 
bash get_dependencies.sh
make

Precompiled binaries are also available for 64-bit Linux systems as follows:

git clone https://github.com/corbinq/apex.git
cd apex/bin
gunzip apex_Linux_x86_64.gz
mv apex_Linux_x86_64 apex && chmod +x apex
./apex --help

Software dependencies

Contact, feedback, bug reports

APEX is a work in progress, and under active development. We appreciate feedback and bug reports, and welcome any questions or feature requests. Contact: qcorbin@hsph.harvard.edu.

Citation

If you use APEX, please cite Quick, C; Guan, L; Lin, X (2020). URL: https://github.com/corbinq/apex (preprint pending). Thanks!

Acknowledgements

APEX is developed by Corbin Quick and Li Guan. Special thanks to