Metadata-Version: 2.1
Name: SpatialDM
Version: 0.0.2
Summary: SpatialDM: Spatial co-expression Detected by bivariate Moran
Home-page: https://github.com/leeyoyohku/SpatialDM
Author: ['Zhouxuan Li', 'Tianjie Wang', 'Yuanhua Huang']
Author-email: leeyoyo@connect.hku.hk
License: Apache-2.0
Description: ===============================================================
        SpatialDM: Spatial Direct Messaging Detected by bivariate Moran
        ===============================================================
        
        About
        =====
        
        
        
        Installation
        ============
        
        SpatialDM is available through `PyPI <https://pypi.org/project/spatialdm/>`_. 
        To install, type the following command line and add ``-U`` for updates:
        
        .. code-block:: bash
        
           pip install -U spatialdm
        
        Alternatively, you can install from this GitHub repository for latest (often 
        development) version by the following command line:
        
        .. code-block:: bash
        
           pip install -U git+https://github.com/leeyoyohku/SpatialDM
        
        Installation time: < 1 min
        
        
        
        Quick example
        =============
        
        Using the build-in melanoma dataset as an example, the following Python script
        will compute the p-value indicating whether a certain Ligand-Receptor is 
        spatially co-expressed.
        
        .. code-block:: python
        
          import spatialdm as sdm
          adata = sdm.datasets.melanoma()
          my_sample = sdm.SpatialDM(X=adata.X, spatialcoord=adata.obsm['spatial'])
          my_sample.extract_lr(species='human', min_cell=3)
          my_sample.weight_matrix(l=1.2, cutoff=0.2, single_cell=False)
          my_sample.spatialdm_global(1000, select_num=None, method='permutation')
          sdm.pl.volcano(my_sample)
        
        
        Detailed Manual
        ===============
        
        The full manual is at https://spatialdm.readthedocs.io
        
        
        References
        ==========
        
        A BioRxiv preprint will be online soon.
Keywords: Spatial transcriptomics,Spatial association,Ligand-recptor interaction
Platform: UNKNOWN
Provides-Extra: docs
