CITL addresses the limitations of the existing methods for inferring time-lagged causal relationships among genes on single-cell RNA sequencing scRNA-seq data. It adopts the changing information of genes estimated by “RNA velocity” for causal inference algorithm. Based on the Time-lagged assumption, CITL can infer time-lagged relationships which are validated by published literature. More information and demonstration is in out article (Wei et al., 2021).
CITL is running in R, a free software environment for statistical computing. R support a wide variety of UNIX platforms, Windows and MacOS, which means that CITL could run on many platforms. The instruction of installing R is at here.
Here is the R package of CITL. If you are working with R only, this version is what you need. However, if you are working across different programming environments, the command-line tool of CITL is more convenient to use. The command-line tool is at https://github.com/wJDKnight/CITL/ . Both the R package and the command-line tool can run independently.
R packages: bnlearn; snow
Use R package: devtools to install CITL.
devtools::install_github("wJDKnight/CITL-Rpackage")
Wei et al.(2021), Inferring time-lagged causality using the derivative of single-cell expression