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)

Installation

Install CACIMAR from github, run:

# 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

Quick tutorial for identifying evolutionally conserved gene regulatory networks

Quick tutorial for identifying evolutionally conserved ligand-receptor interaction and cell-cell communications

Tutorial for build customized orthg database based on MGI

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

Using CACIMAR to analyze retina scRNA-seq data from mouse, zebrafish, and chick

Citation

CACIMAR: Cross-species Analysis of Cell Identities, Markers, Regulations and Interactions Using Single-cell RNA Sequencing Data. (preprint)