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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
`r badger::badge_custom("Seurat", "version4.2", "red", "https://satijalab.org/seurat/articles/get_started.html")`
# 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)**
{ width=70% height=70% }
## Installation
Install CACIMAR from github, run:
``` r
# install.packages("devtools")
devtools::install_github("jiang-junyao/CACIMAR")
```
## News
2024.10.28: remove warning message in 'identify_conserved_marker' function.
2024.10.24: Fixed bugs resulting from a package version update.
2024.08.02: Bugs in 'Identify_CellType' have been fixed.
### Version1.0.0: First version of CACIMAR was published!
## Qucik start (Run CACIMAR in 1 minutes)
For users who want to perform cross-species analysis quickly, we provide a brief tutorial based on small single-cell RNA sequencing (scRNA-seq) data to demonstrate the functionality and API of CACIMAR.
[Quick tutorial for identifying evolutionally conserved celltype and markers based on scRNA-seq data](https://jiang-junyao.github.io/CACIMAR/quick_celltype.html)
[Quick tutorial for identifying evolutionally conserved gene regulatory networks](https://jiang-junyao.github.io/CACIMAR/quick_grn.html)
[Quick tutorial for identifying evolutionally conserved ligand-receptor interaction and cell-cell communications](https://jiang-junyao.github.io/CACIMAR/quick_interaction.html)
[Tutorial for build customized orthg database based on MGI](https://jiang-junyao.github.io/CACIMAR/build_db.html)
## Examples
We also provide comprehensive examples to demonstrate the practical applications of CACIMAR.
[Using CACIMAR to analyze retina scRNA-seq data from mouse and zebrafish](https://jiang-junyao.github.io/CACIMAR/CACIMAR_tutorial)
[Using CACIMAR to analyze retina scRNA-seq data from mouse, zebrafish, and chick](https://jiang-junyao.github.io/CACIMAR/three_species_tutorial)
## Citation
[CACIMAR: Cross-species Analysis of Cell Identities, Markers, Regulations and Interactions Using Single-cell RNA Sequencing Data. (preprint)](https://www.biorxiv.org/content/10.1101/2024.01.23.576964v1)