SCAnalysis

The Single Cell Analysis package includes MAGIC and Wishbone, with additional features (including Palantir)

• Wishbone is an algorithm to align single cells from differentiation systems with bifurcating branches. Wishbone has been designed to work with multidimensional single cell data from diverse technologies such as Mass cytometry and single cell RNA-seq.

• MAGIC (Markov-Affinity Based Graph Imputation of Cells) is an interactive tool to impute missing values in single-cell data and restore the structure of the data. It also provides data preprocessing functionality such as dimensionality reduction and gene expression visualization.

• Palantir

Installation and dependencies

1. SCAnalysis has been implemented in Python3 and can be installed using:

    $> git clone git://github.com/helenjin/scanalysis.git
    $> cd scanalysis
    $> sudo -H pip3 install .
   

2. SCAnalysis depends on a number of python3 packages available on pypi and these dependencies are listed in setup.py. All the dependencies will be automatically installed using the above commands.

3. To uninstall:

    $> sudo -H pip3 uninstall scanalysis
   

Usage

Interactive command line

A tutorial on SCAnalysis usage and results visualization for single cell RNA-seq data can be found in this notebook: https://nbviewer.jupyter.org/github/helenjin/scanalysis/blob/master/notebooks/SCAnalysis.ipynb

GUI

Unfortunately, a python GUI for SCAnalysis is currently unavailable. Updates to follow. However, it would be invoked, like so:

	$> sca_gui.py

Citations

Setty M, Tadmor MD, Reich-Zeliger S, Angel O, Salame TM, Kathail P, Choi K, Bendall S, Friedman N, Pe’er D. "Wishbone identifies bifurcating developmental trajectories from single-cell data." Nat. Biotech. 2016 April 12. http://dx.doi.org/10.1038/nbt.3569

van Dijk, David, et al. "MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data." BioRxiv (2017): 111591. http://www.biorxiv.org/content/early/2017/02/25/111591

Source Code

Wishbone: http://github.com/ManuSetty/wishbone.git

MAGIC: http://github.com/pkathail/magic.git