SISUA
Semi-supervised Single-cell modeling:
- Free software: MIT license
- Documentation: https://github.com/trungnt13/sisua/tree/master/docs.
Reference:
- Trung Ngo Trong, Roger Kramer, Juha Mehtonen, Gerardo González, Ville Hautamäki, Merja Heinäniemi. "SISUA: SemI-SUpervised Generative Autoencoder for Single Cell Data", ICML Workshop on Computational Biology, 2019. [pdf]
Installation
You only need Python 3.6
, the stable version of SISUA installed via pip:
pip install sisua
Install the nightly version on github:
pip install git+https://github.com/trungnt13/sisua@master
For developers, we create a conda environment for SISUA contribution sisua_env
conda env create -f=sisua_env.yml
Getting started
-
- The basics:
-
- Datasets description
- Models specification
- Basic API and work-flow
-
- Single-cell analysis:
-
- Latent space
- Imputation of genes expression
- Prediction of protein markers
-
- Advanced technical topics:
-
- Probabilistic embedding
- Hierarchical modeling (coming soon)
- Causal analysis (coming soon)
- Cross datasets analysis (coming soon)
-
- Benchmarks:
-
- Scalability test
- Fine-tuning networks
- Data normalization
Toolkits
We provide binary toolkits for fast and efficient analyzing single-cell datasets:
- sisua-train: train single-cell modeling algorithms, support training multiple systems in parallel.
- sisua-analyze: evaluate, compare, and interpret trained model.
- sisua-embed: probabilistic embedding for semi-supervised training.
- sisua-data: coming soon
Some important arguments:
-model |
name of function declared in models
|
-ds |
name of dataset declared in data. Description of all predefined datasets is in docs. Some good datasets for practicing:
|
Configuration
By default, the data will be saved at your home folder at ~/bio_data
,
and the experiments' outputs will be stored at ~/bio_log
You can customize these two paths using the environment variables:
- For storing downloaded and preprocessed data:
SISUA_DATA
- For the experiments:
SISUA_EXP
For example:
import os
os.environ['SISUA_DATA'] = '/tmp/bio_data'
os.environ['SISUA_EXP'] = '/tmp/bio_log'
from sisua.data import EXP_DIR, DATA_DIR
print(DATA_DIR) # /tmp/bio_data
print(EXP_DIR) # /tmp/bio_log
or you could set the variables in advance:
export SISUA_DATA=/tmp/bio_data
export SISUA_EXP=/tmp/bio_log
python sisua/train.py
# or using the provided toolkit: sisua-train