README.Rmd

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# CACIMAR: cross-species analysis of cell identities, markers and regulations using single-cell sequencing profiles

CACIMAR has the following 4 main functions:

* **Identify all cell-type specific markers in each species**

* **Identify species-specific or evolutionally conserved markers**

* **Identify conserved intracellular regulations (gene regulatory networks)**

* **Identify conserved intercellular interactions (cell-cell communications)**


![](Readme figure/Workflow.png){ width=70% height=70% }

## Installation


Install CACIMAR from github, run:

``` r
# install.packages("devtools")
devtools::install_github("jiang-junyao/CACIMAR")
```

## News

### Version1.0.0: First version of CACIMAR was published!

## Tutorial

[Using CACIMAR to analyze retina scRNA-seq data from mouse and zebrafish](https://jiang-junyao.github.io/CACIMAR/CACIMAR_tutorial)

## Citation
[Hoang T, Wang J, Boyd P, et al. Gene regulatory networks controlling vertebrate retinal regeneration. Science 2020; 370(6519):eabb8598](https://www.science.org/doi/10.1126/science.abb8598)