Spatial Enrichment Analysis of Gene Association using L-index
Project description
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
Folder
with 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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.