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:
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.
Please check GeneTrajectory tutorial.
References of GeneTrajectory functions can be found here.
Data used in the tutorial can be downloaded from Figshare.
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.