scTM: A pacakge for topic modelling in transcriptomics data
scTM is a package for spatial transcriptomics for single cell that uses topic modelling, solved with stochastic variational infernce. The interesting part is with the formulation of topic models, we can get interpretable embedding which are useful for downstream analysis.
Currently available modules: STAMP
Free software: MIT license
Documentation: https://JinmiaoChenLab.github.io/scTM/.
Features
STAMP: A spatially-aware dimensional reduction designed for spatial data.
Minimal Installation
pip install scTMor
conda create --name sctm python=3.8
git clone https://github.com/JinmiaoChenLab/scTM.git
conda activate sctm
cd scTM
pip install .Basic Usage
Check out our usage of STAMP in the documentation at https://jinmiaochenlab.github.io/scTM/notebooks/stamp/example1/
Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
1 maintainer
Metadata
1 maintainer
Release files for scTM 0.1.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| sctm-0.1.3.tar.gz | 42.6 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| sctm-0.1.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 87.8 kB
Release files / sctm-0.1.3.tar.gz
| Download URL | sctm-0.1.3.tar.gz |
|---|---|
| Size | 42.6 kB |
| Tags | Source |
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Release files / sctm-0.1.3-py3-none-any.whl
| Download URL | sctm-0.1.3-py3-none-any.whl |
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| Size | 45.3 kB |
| Tags | Python 3 |
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