cell-tools is a Single-Cell Data Analysis Toolkit with the following areas of focus and development:

1. scRNA-seq data
2. scATAC-seq data
3. Multiomic (mostly scRNA-seq + scATAC-seq) data

Funtion development will likely focus on scATAC-seq given that there are so many python-implemented tools developed already for scRNA-seq. However, wrappers that enable batch-mode QC and pipeline-oriented solutions have been designed and will eventually be added.

Installation

Install with pip:

pip install cell-tools
# note: limited functionality! for full functionality, install the development (main branch) package! 

Install the development package (main branch):

# (1) clone this repository
git clone https://github.com/mvinyard/cell-tools.git

# (2) install the local project in editable mode
cd ./perturb-tools; pip install -e .

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Disclaimer: There isn't really much of a reason for someone to use this when they would likely be more comfortable using one of the great, well-maintained tools like Scanpy, Seurat, or scvi-tools (or any of the implemented tools, directly). This is mostly a package for personal use, learning, and collaboration. My other goal for this package is to help me version-control and keep track of code that I use frequently.