.. Castl_test documentation master file, created by
   sphinx-quickstart on Thu Jul 31 14:59:47 2025.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Installation
========================

1 Install Castl
------------------------
Python
~~~~~~~~~~~~~~~~~~~~~~~~
``Castl`` can be installed directly from PyPI：

.. code-block:: bash

    pip install STCastl

or download from Github and install it:

.. code-block:: bash

    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.

.. code-block:: r

    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