This is code to perform Poisson regression for Spatial Transcriptomics data as described in this publication:
Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
Emelie Berglund, Jonas Maaskola, Niklas Schultz, Stefanie Friedrich, Maja Marklund, Joseph Bergenstråhle, Firas Tarish, Anna Tanoglidi, Sanja Vickovic, Ludvig Larsson, Fredrik Salmén, Christoph Ogris, Karolina Wallenborg, Jens Lagergren, Patrik Ståhl, Erik Sonnhammer, Thomas Helleday & Joakim Lundeberg
Nature Communications, volume 9, Article number: 2419 (2018)
Whereas you can find here the code for the Negative Binomial regression model described in
Charting Tissue Expression Anatomy by Spatial Transcriptome Deconvolution
Jonas Maaskola, Ludvig Bergenstråhle, Aleksandra Jurek, José Fernández Navarro, Jens Lagergren, Joakim Lundeberg
doi: https://doi.org/10.1101/362624
In order to compile it, you need two libraries:
You build and install the code as follows.
Note that <INSTALL_PREFIX> is a path below which the program will be installed.
This could be e.g. $HOME/local to install into a user-local prefix.
cd build
./gen_build.sh -DCMAKE_INSTALL_PREFIX=<INSTALL_PREFIX>
make
make installThe above will build both a release and a debug version of the code. Please use make release or make debug in place of make above if you want to build only the release or debug version. The binary for the release version will be called std and the binary for the debug version will be called std-dbg.
Note that <INSTALL_PREFIX>/bin and <INSTALL_PREFIX>/lib have to be included in your PATH and LD_LIBRARY_PATH environment variables, respectively.
To do this you have to have lines like the following
export PATH=<INSTALL_PREFIX>/bin:$PATH
export LD_LIBRARY_PATH=<INSTALL_PREFIX>/lib:$LD_LIBRARY_PATHto your $HOME/.bashrc file (or similar in case you are a shell other than bash).
Note that you can find script to analyse the output of this package in another git repository.
