SingleCellFusion is a computational tool to integrate single-cell genomics data. This github repo is the development/pilot implementation of this tool. Code in this repo is used in Luo et al 2019 BioRxiv and in [manuscript in preparation]; it is also expanded into a formal implementation of this tool.
For more information:
- Luo, C. et al. Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants. bioRxiv 2019.12.11.873398 (2019) doi:10.1101/2019.12.11.873398
- Github repo--mukamel-lab/SingleCellFusion
Step 1: Clone this repo.
git clone https://github.com/FangmingXie/SingleCellFusion_dev.git
cd SingleCellFusion_devStep 2: Set up a conda environment and install dependent packages. (Skip this step if not needed.)
conda env create -f environment.yml # create an env named scf_dev
source activate scf_dev./scripts contains the main code.
./example_l5pt contains an example of integrating the layer 5 projection-track (L5 PT) neurons from 4 different datasets from the mouse primary motor cortex ([manuscript in preparation]). The example includes the organized datasets, code, and results, which could be used as a template for other similar tasks.