Spatial Enrichment Analysis of Gene Association using L-index
Install
SEAGAL works for Python3.9, it is advised to create a conda environment with Python3.9 to avoid conflicts of dependencies. Conda installation guide can be found at https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html. After installing conda, run the following command to create a seagal environment:
conda create -n seagal python=3.9
Then install seagal through:
conda activate seagal
conda install -n seagal pip3
pip3 install seagal
Please also install other necessary packages such as jupyter for your research needs.
If Error: module seagal not found occurs when importing, please check if echo $PATH includes the path to python3.9 site packages.
Input data format
- For 10X Visium, Space Ranger
Folderwith the following contents:
- [Folder]/spatial/tissue_positions_list.csv
- [Folder]/filtered_feature_bc_matrix.h5
- CSV-format files:
- count.csv - gene expression data frame in Pandas.DataFrame format.
- meta.csv - spot meta data frame, with x, y columns denoting coordinates.
Running SEAGAL with Visium Data
Please read Tutorial1 for instructions.
Running SEAGAL with user-defined marker genes
Please read Tutorial2 for details.
Running SEAGAL with CSV-format Data
Please read Tutorial3 for details.
Release files for seagal 2.5.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| seagal-2.5.2.tar.gz | 17.4 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| seagal-2.5.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 35.4 kB
Release files / seagal-2.5.2.tar.gz
| Download URL | seagal-2.5.2.tar.gz |
|---|---|
| Size | 17.4 kB |
| Tags | Source |
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Release files / seagal-2.5.2-py3-none-any.whl
| Download URL | seagal-2.5.2-py3-none-any.whl |
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| Size | 18.0 kB |
| Tags | Python 3 |
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Security for seagal 2.5.2
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