locaTE.jl

Cell-specific network inference using local Transfer Entropy.

To get started, please see the documentation.

Code for reproducing the manuscript figures can be found here.

Command line

Command-line script is available in src/locaTE_cmd.jl, which can be called with arguments

usage: locaTE_cmd.jl [--tau TAU] [--k_lap K_LAP] [--lambda1 LAMBDA1]
                     [--lambda2 LAMBDA2] [--outdir OUTDIR]
                     [--suffix SUFFIX] [--cutoff CUTOFF] [--gpu]
                     [--maxiter MAXITER] [-h] [X] [X_rep] [P] [R]

positional arguments:
  X                  path to counts matrix, X
  X_rep              path to dim-reduced representation of X
  P                  path to transition matrix
  R                  path to kernel matrix

optional arguments:
  --tau TAU          power for transition matrix (type: Int64,
                     default: 1)
  --k_lap K_LAP      number of neighbours for Laplacian (type: Int64,
                     default: 15)
  --lambda1 LAMBDA1  (type: Float64, default: 5.0)
  --lambda2 LAMBDA2  (type: Float64, default: 0.01)
  --outdir OUTDIR     (default: "./")
  --suffix SUFFIX     (default: "")
  --cutoff CUTOFF    (type: Float64, default: 0.0)
  --gpu
  --maxiter MAXITER  (type: Int64, default: 1000)
  -h, --help         show this help message and exit

Example:

JULIA_NUM_THREADS=32 julia locaTE_cmd.jl --tau 1 --lambda1 25 --lambda2 0.001 --outdir locaTE_output/ --cutoff 0.3 X.npy X_pca.npy P_velo_dot.npy R.npy 

Examples

For further examples, consult the examples/ directory.

Further information

See the preprint.

Zhang, S.Y. and Stumpf, M.P., 2023. Dynamical information enables inference of gene regulation at single-cell scale. bioRxiv, pp.2023-01.