Repository with some custom utilities for single-cell data analysis.
Check before installing dependencies that will be modified.
pip check git+https://github.com/ktroule/sctools.git
Install repository
pip install git+https://github.com/ktroule/sctools.git
- dotplot_genes: creates a scanpy-based dotplot from a dictionary or dataframe.
- soupy_ratio: calculates the ratio of counts associated to empty droplets compared to all droplets (empty + cells) as called by cellranger.
- calculate_pca: (to be tested). calculates the PCA on the adata without scaling the gene expression.
- load_markers: load set of expression markers.
- pseudobulk_matrix: creates a pseudobulk matrix by aggregating gene counts per user-defined group.
- clean_markers: removes from a dictionary those genes not present in the adata.
To use R with jupyter notebooks you might need to install the following pacakges:
- rpy2==3.4.2
- anndata2ri==1.0.6