Installation

• scLVM is mainly written in python, but we also provide a selft-contained R package. For Mac OS X, we recommend installing the necessary python dependencies using homebrew. For other OS, the following python dependencies are particularly easy to install using the anaconda python distribution:

• Python 2.7 with scipy, h5py, numpy and pylab

• scLVM relies heavily on limix (version 0.6.4 or higher), which can be installed using pip install limix on most systems (see also below if this doesn't work).

• If you would like to use the non-linear GPLVM for visualisation, you we suggest you use the GPy package. This can be installed using pip install GPy

• Preprocessing setps are executed in R and require R>3.0

• If you would like to use the R package you need to install rPython. In case you have several python versions installed on your machine, have a look here on how you can make sure you use the correct version (2.7).

• For a clean Mac OS X install you can try the following commands in the terminal:

  • Set up homebrew:
    • ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
    • brew tap homebrew/python # numpy, scipy, matplotlib etc
    • brew update && brew upgrade
  • Install python: brew install python
  • Install python packages
    • brew install numpy
    • brew install scipy
    • brew install matplotlib
    • brew install hdf5
    • pip install h5py
    • pip install limix (if this does not work, see below for how to install limix from source)
  • Install rPython. As we now have 2 python versions coexisting (the brew one and the native Mac one), we need to tell R to use the correct (brew) version.
    • export RPYTHON_PYTHON_VERSION=2.7.9
    • sudo ln -s /usr/local/Cellar/python/2.7.9/bin/python2.7 /usr/bin/python2.7.9 (for Yosemite, for older OS X you may need to adjust the paths)
    • sudo ln -s /usr/local/Cellar/python/2.7.9/bin/python2.7-config /usr/bin/python2.7.9-config
    • Start R in the console and type: install.packages("rPython", type = "source"). If this gives you errors, you can also simply try install.packages("rPython")
  • Install scLVM:
    • After downloading the scLVM_0.99.1.tar.gz file type: R CMD INSTALL scLVM_0.99.1.tar.gz