Installation

DeltaTopic requires Python 3.8 or later. We recommend to use Miniconda.

PyPI

Install DeltaTopic from PyPI using:

pip install DeltaTopic

Development Version

To work with the latest development version, install from GitHub using:

python3 -m pip install git+https://github.com/causalpathlab/DeltaTopic

Dependencies

• torch, pytroch-lightning - deep learning framework.

• anndata - annotated data object.

• scanpy - toolkit for single-cell analysis.

• numpy, scipy - scientific computing.

Analysis pipeline

The analyis in Zhang et al., 2023 requires the following R packages:

• data.table, dplyr - data wrangling

• goseq, fgsea - gene set enrichment analysis

• ggplot2, ComlexHeatmap, circlize - visualization

To reproduce the analyis in the paper, follow Rmd files in the project repository.

If you run into issues, do not hesitate to approach us or raise a GitHub issue.