TREASMO

TREASMO is a Transcription regulation analysis toolkit for single-cell multi-omics data. It quantifies the single-cell level gene-peak correlation strength, based on which a series of analysis and visualization functions are built to help researchers understand their multi-omics data.

Installation

TREASMO is written in Python and is available from PyPI. Note that Python version should be 3.x.

Install from PyPI

Please run the following command. Creating new environment using conda is recommended.

pip3 install treasmo

# For all the functions, please also install leidenalg and minisom
pip3 install leidenalg
pip3 install minisom

If the above method failed, please try create a new environment using conda first then re-install the three packages above.

If things still doesn't work, try the method below.

Use the package locally

If there is conflicts with other packages or something unexpected happened, try download the package and use it locally in a new conda environment.

# Create a new conda environment
conda create -n treasmo numpy=1.22
conda activate treasmo

# Setting up kernels for Jupyter Notebook if needed
conda install ipykernel
ipython kernel install --user --name=treasmo

# Install dependencies
conda install -c conda-forge scanpy python-igraph leidenalg
conda install -c conda-forge libpysal
conda install -c conda-forge hdf5plugin
conda install -c conda-forge muon
conda install -c conda-forge fa2
conda install -c conda-forge louvain

# Option 1 to install minisom
git clone https://github.com/JustGlowing/minisom.git
cd minisom
python setup.py install

# Option 2 to install minisom
pip3 install minisom

# install Homer if needed

Quick start

• To test whether the package is working without error and go through important functions in TREASMO:

  • Download the toy example data via Google Drive
  • Follow this Jupyter Notebook tutorial to get familiar with the package

• To prepare your own single-cell multiome data for TREASMO, see refer to Notebook here.

Manuscript-related information

• For supplementary materials, please check the Supplementary_Materials folder
• For manuscript results replication, please check the replication folder