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CAESAR suite is an open-source software package that provides image-based spatial co-embedding of locations and genomic features. The ‘CAESAR.Suite’ package is specifically developed by the Jin Liu’s lab for annotation and enrichment analysis of spatially resolved transcriptomics (SRT) dataset. It uniquely transfers labels from scRNA-seq reference, enabling the annotation of spatial omics datasets across different technologies, resolutions, species, and modalities, based on the conserved relationship between signature genes and cells/locations at an appropriate level of granularity. Notably, CAESAR enriches location-level pathways, allowing for the detection of gradual biological pathway activation within spatially defined domain types.
Check out our Package Website for a more complete description of the methods and analyses.
CAESAR provides image-based spatial aware co-embedding of locations and genomic features.
By assuming a conserved relationship between genomic features and cells/locations within each cell/domain type at an appropriate level of granularity, the CAESAR suite flexibly annotates spatial omics datasets in a variety of contexts, for instance:
The CAESAR suite includes functions for hypothesis testing to identify pathways enriched in each cell/location or cell/domain type. For instance:
In addition, once the co-embeddings of (multiple) dataset are estimated by CAESAR, the package provides functionality for further data exploration, analysis, and visualization. Users can:
“CAESAR.Suite” depends on the Rcpp and RcppArmadillo package, which requires appropriate setup of computer. For the users that have set up system properly for compiling C++ files, the following installation command will work.
# Method 1: Install CAESAR.Suite from CRAN
install.packages('CAESAR.Suite')
# For the newest version of CAESAR.Suite, users can use method 2 for installation.
# Method 2: Install CAESAR.Suite from Github
if (!require("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github("XiaoZhangryy/CAESAR.Suite")
# If some dependent packages (such as `scater`) on Bioconductor cannot be installed normally, use the following commands, then run the above command.
if (!require("BiocManager", quietly = TRUE)) ## install BiocManager
install.packages("BiocManager")
# Install the package on Bioconductor
BiocManager::install(c("scater"))For usage examples and guided walkthroughs, check the vignettes directory of the repo.
Tutorials for CAESAR suite:
For the users that don’t have set up system properly, the following setup on different systems can be referred. ## Setup on Windows system First, download Rtools; second, add the Rtools directory to the environment variable.
First, install Xcode. Installation about Xcode can be referred here.
Second, install “gfortran” for compiling C++ and Fortran at here.
If you use conda environment on Linux system and some dependent packages (such as scater) can not normally installed, you can search R package at anaconda.org website. We take the scater package as example, and its search result is https://anaconda.org/bioconda/bioconductor-scater. Then you can install it in conda environment by following command.
conda install -c bioconda bioconductor-scaterFor the user not using conda environment, if dependent packages (such as scater) not normally installed are in Bioconductor, then use the following command to install the dependent packages.
# install BiocManager
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# install the package on Bioconducter
BiocManager::install(c("scater"))If dependent packages (such as ProFAST) not normally installed are in CRAN, then use the following command to install the dependent packages.
# install the package on CRAN
install.packages("ProFAST")For an example of typical CAESAR.Suite usage, please see our Package Website for a demonstration and overview of the functions included in CAESAR.Suite.