Installation

1 Install Castl

Python

Castl can be installed directly from PyPI：

pip install STCastl

or download from Github and install it:

git clone https://github.com/TheY11/Castl

cd Castl
pip install -e .

R

We also provide the R package `castlRUtils` for calculating quality scores (QS) of SVGs.

library(devtools)
devtools::install_github("TheY11/Castl", subdir = "Castl/r_utils", force = TRUE)
library(castlRUtils)

2 System Dependencies

Python >= 3.9.5

• pandas >= 1.3.0

• numpy >= 1.21.0

• rpy2 >= 3.5.0

• scipy >= 1.7.0

• statsmodels >= 0.13.0

• anndata >= 0.8.0

• scanpy >= 1.9.0

• matplotlib >= 3.5.0

• seaborn >= 0.12.0

• scikit-learn >= 1.0.0

R >= 4.0.5

• dplyr >= 1.0.0

• tidyverse >= 1.3.0

• clusterProfiler >= 3.18.0

• org.Hs.eg.db >= 3.12.0

• patchwork >= 1.1.0

• ggplot2 >= 3.3.0

• TissueEnrich >= 1.8.0

• SummarizedExperiment >= 1.20.0