Python and R code facilitating the alignment of trajectories using a combination of determined marker genes, pseudotime assignment from a trajectory inference method, and dynamic time warping.
To use clone the repo to some/dir, for an R utility use source(some/dir/traj-branch-align/src/R/r_util_of_interest.r) in your R environment. For a python utility add some/dir/traj-branch-align/src/python to your $PYTHONPATH. Make sure the dependencies for the particular utility (listed below) are installed.
R - branch_gene_markers.r
install.packages("gam")