KlugerLab / GeneTrajectory

R implementation of GeneTrajectory

Gene Trajectory Inference

GeneTrajectory is a method for inferring gene trajectories in scRNA-seq data, which facilitates understanding of gene dynamics underlying biological processes. The major workflow of GeneTrajectory comprises the following four main steps:

• Step 1. Build a cell-cell kNN graph in which each cell is connected to its k-nearest neighbors. Find the shortest path connecting each pair of cells in the graph and denote its length as the graph distance between cells.
• Step 2. Compute pairwise graph-based Wasserstein distance between gene distributions, which quantifies the minimum cost of transporting the distribution of a given gene into the distribution of another gene in the cell graph.
• Step 3. Generate a low-dimensional representation of genes (using Diffusion Map by default) based on the gene-gene Wasserstein distance matrix. Identify gene trajectories in a sequential manner.
• Step 4. Determine the order of genes along each gene trajectory.

Install

GeneTrajectory can be installed in R as follows:

install.packages("devtools")
devtools::install_github("KlugerLab/GeneTrajectory")

A Python implementation is available at https://github.com/KlugerLab/GeneTrajectory-python.

Example tutorial

Please check GeneTrajectory tutorial.

References

References of GeneTrajectory functions can be found here.

Data used in the tutorial can be downloaded from Figshare.

Install GeneTrajectory-python

The easiest way is to create a virtualenv for gene_trajectory using reticulate

if(!reticulate::virtualenv_exists('gene_trajectory')){
  reticulate::virtualenv_create('gene_trajectory', packages=c('gene_trajectory'))
}
reticulate::use_virtualenv('gene_trajectory')

or to add to an existing virtualenv using

reticulate::py_install("gene-trajectory")

In general (especially in a conda environment) it can be installed with pip as

system(sprintf('%s -m pip install gene-trajectory', reticulate::py_exe()))

The development version can be installed as

system(sprintf('%s -m pip install git+https://github.com/Klugerlab/GeneTrajectory-python.git', reticulate::py_exe()))

This works both on virtualenv and conda.