gsMap 1.62__tar.gz → 1.64__tar.gz

{gsmap-1.62 → gsmap-1.64}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gsMap
-Version: 1.62
+Version: 1.64
 Summary: Genetics-informed pathogenic spatial mapping
 Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
 Requires-Python: >=3.8
@@ -26,6 +26,12 @@ Requires-Dist: pyranges
 Requires-Dist: pyfiglet
 Requires-Dist: plotly
 Requires-Dist: kaleido
+Requires-Dist: jinja2
+Requires-Dist: scanpy
+Requires-Dist: zarr
+Requires-Dist: bitarray
+Requires-Dist: pyarrow
+Requires-Dist: scikit-misc
 Requires-Dist: sphinx ; extra == "doc"
 Requires-Dist: sphinx-argparse ; extra == "doc"
 Requires-Dist: sphinx-autobuild ; extra == "doc"
@@ -46,21 +52,22 @@ Requires-Dist: sphinxcontrib-serializinghtml ; extra == "doc"
 Requires-Dist: furo ; extra == "doc"
 Requires-Dist: myst-parser ; extra == "doc"
 Requires-Dist: nbsphinx ; extra == "doc"
-Project-URL: Documentation, https://...
+Project-URL: Documentation, https://yanglab.westlake.edu.cn/gsmap/document
 Project-URL: Home, https://github.com/LeonSong1995/gsMap
-Project-URL: Website, https://...
+Project-URL: Website, https://yanglab.westlake.edu.cn/gsmap/home
 Provides-Extra: doc
 
 # gsMap (genetically informed spatial mapping of cells for complex traits)
-[![stars-badge](https://img.shields.io/github/stars/LeonSong1995/MeDuSA?logo=GitHub&color=yellow)](https://github.com/LeonSong1995/gsMap/stargazers)
+[![stars-badge](https://img.shields.io/github/stars/LeonSong1995/gsMap?logo=GitHub&color=yellow)](https://github.com/LeonSong1995/gsMap/stargazers)
+[![pypi-badge](https://img.shields.io/pypi/v/gsMap)](https://pypi.org/p/gsMap)
 [![license-badge](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
+![Model architecture](schematic.png)
 
-## Features
+## 1.Citation
+Liyang Song, Wenhao Chen, Junren Hou, Minmin Guo, Jian Yang (2024) Spatially resolved mapping of cells associated with human complex traits. (Under review)
 
-....
-
-## Installation
+## 2.Installation
 
 install use pip:
 
@@ -71,52 +78,20 @@ pip install gsMap
 install from source:
 
 ```bash
-git clone
+git clone https://github.com/LeonSong1995/gsMap.git
 cd gsMap
 pip install -e .
 ```
 
-## Usage
-
-To use gsMap, navigate to the command line and enter `gsMap` followed by the subcommand that corresponds to the desired operation. Each subcommand may require specific arguments to run.
-
-### Basic Command Structure
-
-```bash
-gsmap subcommand [arguments...]
-```
-
-- `subcommand`: The specific operation you wish to perform.
-- `arguments`: The arguments and options required for the subcommand.
-
-### Available Subcommands
-
-(Provide a list and brief description of each available subcommand. For example:)
-
-- `run_find_latent_representations`: Finds latent representations using a GNN-VAE model.
-- `run_latent_to_gene`: Maps latent representations to gene markers.
-- `run_generate_ldscore`: Generates LD scores for genomic spots.
-- `run_spatial_ldsc`: Conducts spatial LDSC analysis.
-- `run_cauchy_combination`: Performs Cauchy combination tests for annotations.
-- `run_all_mode`: Executes a comprehensive pipeline covering all steps.
-
-### Examples
-
-To run a specific functionality, you need to provide the appropriate subcommand and arguments. For example:
-### Running Requirement
-
-
-```bash
-gsmap run_find_latent_representations --input_hdf5_path <path> --output_hdf5_path <path> --sample_name <name>
-```
+## 3.Usage
 
-This command initiates the process of finding latent representations based on the given HDF5 input and output paths and sample name.
+Please checkout the documentations and tutorials at
+[gsMap.docs](https://yanglab.westlake.edu.cn/gsmap/document).
 
-## Contributing
 
-...
+## 4.Online visualization
 
-## License
+To visualize the traits-embryo or traits-brain association spatial maps, please refer to [gsmap.visualization](https://yanglab.westlake.edu.cn/gsmap/visualize).
 
 ....
 

gsmap-1.64/README.md

@@ -0,0 +1,39 @@
+# gsMap (genetically informed spatial mapping of cells for complex traits)
+[![stars-badge](https://img.shields.io/github/stars/LeonSong1995/gsMap?logo=GitHub&color=yellow)](https://github.com/LeonSong1995/gsMap/stargazers)
+[![pypi-badge](https://img.shields.io/pypi/v/gsMap)](https://pypi.org/p/gsMap)
+[![license-badge](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+![Model architecture](schematic.png)
+
+## 1.Citation
+Liyang Song, Wenhao Chen, Junren Hou, Minmin Guo, Jian Yang (2024) Spatially resolved mapping of cells associated with human complex traits. (Under review)
+
+## 2.Installation
+
+install use pip:
+
+```bash
+pip install gsMap
+```
+
+install from source:
+
+```bash
+git clone https://github.com/LeonSong1995/gsMap.git
+cd gsMap
+pip install -e .
+```
+
+## 3.Usage
+
+Please checkout the documentations and tutorials at
+[gsMap.docs](https://yanglab.westlake.edu.cn/gsmap/document).
+
+
+## 4.Online visualization
+
+To visualize the traits-embryo or traits-brain association spatial maps, please refer to [gsmap.visualization](https://yanglab.westlake.edu.cn/gsmap/visualize).
+
+....
+
+---