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.