nlvelo (nonlinear velocyto) is R package for RNA velocity estimation using nonlinear models, which was rebulit based on the original velocyto package.
Check out our paper in Cell Reports (Haensel and Jin et al. 2020) for the detailed methods and its application to the Epidermal Basal Cell States Transition Dynamics During Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics.
La Manno et al. used a linear model to relate abundance of pre-mRNA U(t) with abundance of mature mRNA S(t) (La Manno et al., Nature 2018). Given that the molecular regulatory mechanisms between pre-mRNA and mature mRNA are complicated, and in many molecular networks more commonly we observe non-linear (e.g. switch-like) responses, we proposed a nonlinear model of RNA velocity for the effects of pre-mRNA on the abundance of mature mRNA based on Michaelis–Menten kinetics.
Similar to velocyto.R package, nlvelo requires the following key elements:
- C++11
- Open MP support
- boost libaries
- igraph library
- hdf5c++ library (as required by the h5 R package to support loom files)
The easiest way to install nlvelo is using devtools::install_github():
library(devtools)
devtools::install_github("sqjin/nlvelo")
You need to have boost (e.g. sudo apt-get install libboost-dev) and openmp libraries installed. Please see detailed installation commands here.
- nlvelo demo
- Interface with other single-cell analysis toolkits (e.g., Seurat)
- Generate a .loom file from .bam/.sam files
If you have any problems, comments or suggestions, please contact us at Suoqin Jin (suoqin.jin@uci.edu).