PEER (probabilistic estimation of expression residuals) is a tool to determine hidden factors from expression data, for use in genetic association studies such as eQTL mapping.
The method is first discussed in a 2010 PLOS Comp Bio paper:
and a guide to its applications and use in a 2012 Nature Protocols paper:
To install a command line version of the tool, you can clone it from the github page
git clone https://github.com/PMBio/peer
When installing, it won’t install the executable binary peertool by default, nor will it use a user directory as the install location (though the latter is addressed at the end of documentation). To install these, use the following commands:
cd peer && mkdir build && cd build
cmake -D CMAKE_INSTALL_PREFIX=~/software -D BUILD_PEERTOOL=1 ./..
Which will install peertool to ~/software/bin, which you can put on your path.