gsMap 1.72.3__py3-none-any.whl → 1.73.0__py3-none-any.whl

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Files changed (18) hide show
  1. gsMap/__init__.py +1 -1
  2. gsMap/cauchy_combination_test.py +5 -5
  3. gsMap/config.py +141 -21
  4. gsMap/create_slice_mean.py +32 -18
  5. gsMap/find_latent_representation.py +1 -1
  6. gsMap/format_sumstats.py +6 -0
  7. gsMap/generate_ldscore.py +8 -40
  8. gsMap/latent_to_gene.py +42 -14
  9. gsMap/run_all_mode.py +1 -0
  10. gsMap/utils/generate_r2_matrix.py +13 -292
  11. gsMap/utils/regression_read.py +0 -76
  12. gsmap-1.73.0.dist-info/METADATA +169 -0
  13. gsmap-1.73.0.dist-info/RECORD +31 -0
  14. {gsmap-1.72.3.dist-info → gsmap-1.73.0.dist-info}/WHEEL +1 -1
  15. {gsmap-1.72.3.dist-info → gsmap-1.73.0.dist-info/licenses}/LICENSE +6 -6
  16. gsmap-1.72.3.dist-info/METADATA +0 -120
  17. gsmap-1.72.3.dist-info/RECORD +0 -31
  18. {gsmap-1.72.3.dist-info → gsmap-1.73.0.dist-info}/entry_points.txt +0 -0
gsmap-1.72.3.dist-info/METADATA DELETED
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- Metadata-Version: 2.3
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- Name: gsMap
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- Version: 1.72.3
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- Summary: Genetics-informed pathogenic spatial mapping
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- Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
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- Requires-Python: >=3.8
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- Description-Content-Type: text/markdown
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- Classifier: Development Status :: 3 - Alpha
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- Classifier: Intended Audience :: Developers
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- Classifier: License :: OSI Approved :: MIT License
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- Classifier: Programming Language :: Python :: 3.8
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- Classifier: Programming Language :: Python :: 3.9
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- Classifier: Operating System :: POSIX :: Linux
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- Requires-Dist: numpy < 2.0.0
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- Requires-Dist: pandas
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- Requires-Dist: scipy
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- Requires-Dist: scikit-learn
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- Requires-Dist: matplotlib
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- Requires-Dist: seaborn
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- Requires-Dist: tqdm
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- Requires-Dist: pyyaml
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- Requires-Dist: torch
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- Requires-Dist: torch-geometric
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- Requires-Dist: pyranges
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- Requires-Dist: pyfiglet
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- Requires-Dist: plotly
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- Requires-Dist: kaleido
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- Requires-Dist: jinja2
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- Requires-Dist: scanpy >=1.8.0
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- Requires-Dist: zarr
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- Requires-Dist: bitarray >=2.9.2, <3.0.0
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- Requires-Dist: pyarrow
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- Requires-Dist: scikit-misc
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- Requires-Dist: sphinx ; extra == "doc"
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- Requires-Dist: sphinx-argparse ; extra == "doc"
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- Requires-Dist: sphinx-autobuild ; extra == "doc"
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- Requires-Dist: sphinx-autodoc-typehints ; extra == "doc"
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- Requires-Dist: sphinx-basic-ng ; extra == "doc"
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- Requires-Dist: sphinx-charts ; extra == "doc"
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- Requires-Dist: sphinx-copybutton ; extra == "doc"
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- Requires-Dist: sphinx_inline_tabs ; extra == "doc"
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- Requires-Dist: sphinx-markdown-tables ; extra == "doc"
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- Requires-Dist: sphinx-rtd-theme ; extra == "doc"
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- Requires-Dist: sphinxcontrib-applehelp ; extra == "doc"
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- Requires-Dist: sphinxcontrib-devhelp ; extra == "doc"
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- Requires-Dist: sphinxcontrib-htmlhelp ; extra == "doc"
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- Requires-Dist: sphinxcontrib-jquery ; extra == "doc"
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- Requires-Dist: sphinxcontrib-jsmath ; extra == "doc"
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- Requires-Dist: sphinxcontrib-qthelp ; extra == "doc"
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- Requires-Dist: sphinxcontrib-serializinghtml ; extra == "doc"
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- Requires-Dist: furo ; extra == "doc"
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- Requires-Dist: myst-parser ; extra == "doc"
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- Requires-Dist: nbsphinx ; extra == "doc"
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- Project-URL: Documentation, https://yanglab.westlake.edu.cn/gsmap/document/software
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- Project-URL: Home, https://github.com/LeonSong1995/gsMap
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- Project-URL: Website, https://yanglab.westlake.edu.cn/gsmap/home
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- Provides-Extra: doc
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-
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- [![GitHub Stars](https://img.shields.io/github/stars/JianYang-Lab/gsMap?logo=GitHub&color=yellow)](https://github.com/LeonSong1995/gsMap/stargazers)
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- [![PyPI Version](https://img.shields.io/pypi/v/gsMap)](https://pypi.org/project/gsMap)
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- [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
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-
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- # gsMap
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-
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- ## Introduction
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-
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- `gsMap` (genetically informed spatial mapping of cells for complex traits)
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- integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS)
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- summary statistics to map cells to human complex traits, including diseases,
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- in a spatially resolved manner.
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-
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- ## Key Features
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-
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- - **Spatially-aware High-Resolution Trait Mapping**
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- - **Spatial Region Identification**
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- - **Putative Causal Genes Identification**
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-
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- ![Model Architecture](schematic.png)
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-
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- ## Installation
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-
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- Install using pip:
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-
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- ```bash
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- conda create -n gsMap python>=3.10
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- conda activate gsMap
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- pip install gsMap
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- ```
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-
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- Install from source:
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-
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- ```bash
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- git clone https://github.com/LeonSong1995/gsMap.git
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- cd gsMap
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- pip install -e .
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- ```
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-
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- Verify the installation by running the following command:
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-
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- ```bash
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- gsmap --help
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- ```
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-
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- ## Usage
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-
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- Please check out the documentation and tutorials at [gsMap Documentation](https://yanglab.westlake.edu.cn/gsmap/document/software).
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-
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- ## Online Visualization
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-
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- To visualize the traits-cell association spatial maps,
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- please refer to [gsMap Visualization](https://yanglab.westlake.edu.cn/gsmap/visualize).
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-
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- ## Citation
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-
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- Song, L., Chen, W., Hou, J., Guo, M. & Yang, J.
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- [Spatially reso lved mapping of cells associated with human complex traits.](https://www.medrxiv.org/content/10.1101/2024.10.31.24316538v1)
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- medRxiv, 2024.2010.2031.24316538 (2024) (Nature in press).
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-
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- Please cite the paper and give us a STAR if you find gsMap useful for your research.
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-
gsmap-1.72.3.dist-info/RECORD DELETED
@@ -1,31 +0,0 @@
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- gsMap/__init__.py,sha256=KG_fjg3SKMr0pH9IBYN_dW9c_Rwhr3YDkWc_b5jnEzw,77
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- gsMap/__main__.py,sha256=Vdhw8YA1K3wPMlbJQYL5WqvRzAKVeZ16mZQFO9VRmCo,62
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- gsMap/cauchy_combination_test.py,sha256=zT-XFCZJMOMu7sXYZ2n7DE1XKd4lYB-5q0ZSAcQlcfY,5075
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- gsMap/config.py,sha256=kJa7uacKzLebCFPo0y1q8NjQXqla8V1nIE7MCXQu8XA,47020
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- gsMap/create_slice_mean.py,sha256=X4GzvoFeRyAPmdifODT6NRNTk4nfC0KrYfOHeMjPBLk,5585
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- gsMap/diagnosis.py,sha256=RcoIQoK2rtHpEqmSVwOG_amfKWuu1r5T8e2POPfIpOM,13362
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- gsMap/find_latent_representation.py,sha256=wFY74YoZMSa7--2yrf4zYHYxqP0gtIrcNCKgcPojoPQ,4738
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- gsMap/format_sumstats.py,sha256=8k-axws38NgRmJ69cnQtYZFdTsHdhBP0aBt4zHgU5vs,13610
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- gsMap/generate_ldscore.py,sha256=tLU9u6yl37AXVrOxeCxKKWQtDy8YZf9BMRPEQzfLPrc,29113
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- gsMap/latent_to_gene.py,sha256=1xdQJxkZ83PvinKXlcyllywxmfyCUt6y9xDksVNCBkc,11160
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- gsMap/main.py,sha256=SzfAXhrlr4LXnSD4gkvAtUUPYXyra6a_MzVCxDBZjr0,1170
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- gsMap/report.py,sha256=_1FYkzGhVGMnvHgEQ8z51iMrVEVlh48a31jLqbV2o9w,6953
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- gsMap/run_all_mode.py,sha256=N_5J6Zbl2eJjVK0OXDzU8hZwxrakQS-3WeDIlKg0zWI,9289
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- gsMap/setup.py,sha256=lsIQCChHwR0ojWZs7xay8rukRaLlueuLkc83bp-B2ZE,103
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- gsMap/spatial_ldsc_multiple_sumstats.py,sha256=-mawOBjn8-Y5Irl8mv8ye83hfiEJ1mkLrRIQiI-XaMM,17973
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- gsMap/visualize.py,sha256=N55s-xmzSd_DtIesrGewfDeoytYUcMd2acDsjEpChCA,7242
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- gsMap/GNN/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- gsMap/GNN/adjacency_matrix.py,sha256=MfkhgpAHJcC-3l_iZDQQYD30w4bpe29-8s6kkGxiwQw,3231
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- gsMap/GNN/model.py,sha256=75In9sxBkaqqpCQSrQEUO-zsQQVQnkXVbKsAgyAZjiQ,2918
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- gsMap/GNN/train.py,sha256=S6s-AufN9GJNcgC5Mqe6MjcJAsaNnbDlHUoYHcvxFmA,3069
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- gsMap/templates/report_template.html,sha256=QODZEbVxpW1xsLz7lDrD_DyUfzYoi9E17o2tLJlf8OQ,8016
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- gsMap/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- gsMap/utils/generate_r2_matrix.py,sha256=uYy4sbYm5Uwn875hPG85y-3ZjBYmE_eGHpHcdFGKaag,28541
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- gsMap/utils/jackknife.py,sha256=w_qMj9GlqViouHuOw1U80N6doWuCTXuPoAVU4P-5mm8,17673
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- gsMap/utils/manhattan_plot.py,sha256=N7jd0Cn-7JMsTBgv41k1w0174rqnPT-v7xLIV2cfY5U,25241
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- gsMap/utils/regression_read.py,sha256=YbRPktMf9-wM7QqUHYZw8Kcr3LKEGQSLsAT9AMhUe5w,7782
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- gsmap-1.72.3.dist-info/entry_points.txt,sha256=s_P2Za22O077tc1FPLKMinbdRVXaN_HTcDBgWMYpqA4,41
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- gsmap-1.72.3.dist-info/LICENSE,sha256=dCWx-ENipnYph2UTEA9wJaEZ_tkjNZ_tog6XRd3nd2k,1073
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- gsmap-1.72.3.dist-info/WHEEL,sha256=CpUCUxeHQbRN5UGRQHYRJorO5Af-Qy_fHMctcQ8DSGI,82
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- gsmap-1.72.3.dist-info/METADATA,sha256=jCdwjCz28iEmPzJx7bRQ70cnASPFST2E05FZUfP_94I,4076
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- gsmap-1.72.3.dist-info/RECORD,,