PicturedRocks–Single Cell RNA-seq Analysis Tool

PicturedRocks is a tool for the analysis of single cell RNA-seq data. Currently, we implement two marker selection approaches:

  • a 1-bit compressed sensing based sparse SVM algorithm, and
  • a mutual information-based greedy feature selection algorithm.


Please ensure you have Python 3.6 or newer and have numba and scikit-learn installed. The best way to get Python and various dependencies is with Anaconda or Miniconda. Once you have a conda environment, run conda install numba scikit-learn. Then use pip to install PicturedRocks and all additional dependencies:

pip install picturedrocks

To install the latest code from github, clone our github repository. Once inside the project directory, instal by running pip install -e .. The -e option will point a symbolic link to the current directory instead of installing a copy on your system.

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