Getting started

Please refer to the documentation, in particular the sections

• Preparing data

• Creating signatures, and

• Testing signatures.

If you want to implement own methods for creating and testing signatures, please take a look at the

• Developer’s guide and the

• API documentation.

Installation

You need to have Python 3.7 or newer installed on your system. Some methods for creating or testing signatures additionally require R. If you don’t have Python installed, we recommend installing Miniforge.

There are several alternative options to install pygenesig:

1. Install pygenesig in a self-contained conda environment:

   This is the most reliable option to make both R and Python work. Make sure you have the `conda-forge` and the `bioconda` channels set-up with the correct priorities as described in the Bioconda documentation.

   # use `mamba` instead of `conda` for more speed
   mamba create -n pygenesig python=3.8 pip bioconductor-edger bioconductor-bioqc
   conda activate pygenesig
   pip install pygenesig

2. Install pygenesig via pip and R packages manually

   pip install pygenesig

   Then, in R:

   install.packages("BiocManager")
   BiocManager::install(c("edgeR", "BioQC"))

   Usually, if R is in your PATH, rpy2 automatically detects your R installation. If you get an error message while importing pygensig, try setting the R_HOME environment variable before importing pygenesig:

   import os
   os.environ["R_HOME"] = "/usr/lib/R"
   import pygenesig

3. Install the latest development version from GitHub:

   pip install git+https://github.com/grst/pygenesig.git@master

   You’ll need to separately install R packages as described above.

Release notes

See the release section.

Contact

Please use the issue tracker.