This is a modified version of the Mosaic project originally written by Mission Bio to analyze single-cell DNA and protein data generated by the Tapestri instrument. The tool has been customized for the analysis in Zhang et al. (2022) [https://doi.org/10.1101/2022.03.06.483206]. Most importantly, the genotyping module has been customized for study of tumor samples.
The software has been tested on MacOS 11.2.1 and Linux CentOS7.
Dependencies are detailed in conda-requirements.yml. Some of the plotting packages might cause conflict on certain systems, and their version requirement could be relaxed, although this has not been formally tested.
Clone this repository into your working directory with
git clone https://github.com/haochenz96/mosaic
It is highly recommended to install all the dependencies with Conda.
First, create a Conda environment with the configuration file conda-requirements.yml:
conda env create -f conda-requirements.yml
By default, this will create a new environment called mosaic, which can be activated with:
conda activate mosaic
Install the mosaic package to the environment with:
pip install -e /path/to/mosaic
Typical installation time is under 15 min on a normal desktop computer. If it takes longer, it is likely due to some of the plotting dependencies causing conflicts and their version requirements may be relaxed.
It is highly recommended to install TEA, which provides a set of utility tools for analyzing Tapestri data, along with Mosaic. Please note this package is under active development, so to replicate the results in Zhang et al., (2022), please use the frozen branch ncomm_2022_publication.
It an be obtained from Github and then installed via pip:
git clone https://github.com/haochenz96/tea.git
pip install -e /path/to/tea
Jupyter notebooks demonstrating the customized functionalities in this version of mosaic are placed in tutorials/. Example data is placed in data/.
For more comprehensive documentation on data structure and more functions, please refer to Mission Bio's documentation:
- Data structure: https://missionbio.github.io/mosaic/v1.8.0/index.html
- Usage Vignettes: https://github.com/MissionBio/mosaic-jupyter