CASi: Cross-timepoint Analysis of Single-cell RNA sequencing data
| CASi is a comprehensive R package for analyzing multi-timepoint scRNA-seq data, which provides users with: (1) cross-time points cell annotation, (2) detection of potentially novel cell types emerged over time, (3) visualization of cell population evolution, and (4) identification of temporal differentially expressed genes (tDEGs). |
Installation
The installation instructions are the same for both MacOS users and Windows users. In R:
require(devtools)
devtools::install_github("yizhuo-wang/CASi")Alternatively, you can download the zip file and install it from using:
install.packages("file_name_and_path", repos = NULL, type="source")OR, in RStudio, you can download the zip file and open the CASi.Rproj to install the whole package.
Usage
Before using CASi, please make sure to set up TensorFlow from https://tensorflow.rstudio.com/install/, and that the dependent package "keras" is available to use.
require(keras)
require(CASi)Input
- Gene expression matrix of the initial data point/t0.
- Gene expression matrix of the following data points/t1.
- (optional) Cell labels of the initial data point.
Vignettes
A thorough demonstration can be found at https://github.com/yizhuo-wang/CASi/blob/vignettes/CASi.html.
To-do
- Publish on Bioconductor.