/sctools

A set of tool for single-cell analysis.

Primary LanguagePython

sctools

Repository with some custom utilities for single-cell data analysis.

Instructions to install

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

Modules

Visualization

  • dotplot_genes: creates a scanpy-based dotplot from a dictionary or dataframe.

Metrics

  • soupy_ratio: calculates the ratio of counts associated to empty droplets compared to all droplets (empty + cells) as called by cellranger.

Tools

  • 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.

Notes

To use R with jupyter notebooks you might need to install the following pacakges:

  • rpy2==3.4.2
  • anndata2ri==1.0.6