LVPT

LVPT (Lazy velocity pseudotime) is a trajectory inference method for single cell RNA-seq data.

Prepare

To run lvpt, please install following softwares:

• scanpy
• scvelo
• dynverse
• docker (To make sure the dynmethod can run)

Start

Import Lvpt files.

import lvpt

from velocity_graph import velocity_graph

Use following code to calculate lazy velocity pseudotime.

velocity_graph(adata, steady = 0.05)

lvpt.velocity_pseudotime(adata, root_key='cell9')

Examples

File name	Description
main.py	The example experiment of pancreas dataset.
dentategyus.py	The example experiment of dentategyus dataset.
evaluation.py & evaluation.R	The examples of simulated datasets.