https://github.com/isolationkernel/kernel-bounded-clustering-for-spatial-transcriptomics
https://github.com/isolationkernel/kernel-bounded-clustering-for-spatial-transcriptomics
Last synced: 4 months ago
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- Host: GitHub
- URL: https://github.com/isolationkernel/kernel-bounded-clustering-for-spatial-transcriptomics
- Owner: IsolationKernel
- Created: 2024-07-16T11:19:18.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-07-16T13:05:17.000Z (over 1 year ago)
- Last Synced: 2025-06-07T12:33:07.346Z (8 months ago)
- Language: Python
- Size: 30.3 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Kernel-Bounded-Clustering-for-Spatial-Transcriptomics
# Installation
## python 3.8+
```
pip install scikit-learn
pip install h5py
pip install pandas
pip install python-igraph
pip install scanpy
```
## Matlab install the toolbox:
1. Parallel Computing Toolbox
2. Statistics and Machine Learning Toolbox
# Dataset
The datasets in the turtorial are already preprocessed, download it from the following link and move it to the current directory tutorial/Dataset
https://drive.google.com/drive/folders/1MziiMAcUQeXwX8kvKaYmmoZBkzmohrlH?usp=drive_link
and the original dataset can be downloaded from the following link.
### DLPFC
http://spatial.libd.org/spatialLIBD/
### HER2st
https://github.com/almaan/her2st
### Slide-seq V2 mouse hippocampus
https://singlecell.broadinstitute.org/single_cell/study/SCP815/sensitive-spatial-genome-wideexpression-profiling-at-cellular-resolution#study-summary
### Stereo-seq mouse olfactory bulb
https://github.com/JinmiaoChenLab/SEDR_analyses
# DLPFC
1. cd /tutorial/wlikbc
2. Run DLPFC_WL.py
3. Open Matlab and run the file turtorial/KBC/DLPFC_KBC.m
# HER2st
1. cd /tutorial/wlikbc
2. Run HER2stWL.py
3. Open Matlab and run the file turtorial/KBC/HER2st_KBC.m
# Slide-seq V2 mouse hippocampus
1. cd /tutorial/wlikbc
2. Run slideseqv2norwl.py
3. Open Matlab and run the file turtorial/KBC/Slideseqv2_KBC.m
# Stereo-seq mouse olfactory bulb
1. cd /tutorial/wlikbc
2. Run sterseqwl.py
3. Open Matlab and run the file turtorial/KBC/sterseq_KBC.m
4. cd /tutorial/wlikbc and run plot_stereo.py