inferploidy 0.3.0

Tookits for Tumor cell identification in single-cell RNA-seq data

InferPloidy

Brief introduction

• InferPloidy is a CNV-based, ploidy annotation tool for single-cell RNA-seq data.
• It works with the CNV-estimates obtained from infercnv .

Cite InferPloidy

• "InferPloidy: A fast ploidy inference tool accurately classifies cells with abnormal CNVs in large single-cell RNA-seq datasets", available at bioRxiv

Installation using pip, importing inferploidy in Python

InferPloidy can be installed using pip command. With python3 installed in your system, simply use the follwing command in a terminal.

pip install inferploidy

Once it is installed using pip, you can import two functions using the following python command.

from inferploidy import run_infercnv, run_inferploidy

Example usage in Jupyter notebook

inferPloidy_example.ipynb is example code in Jupyter notebook, where you can see how to import and run InferPloidy.

To run HiCAT, you need the pre-installed python packages numpy, pandas, scikit-learn, scipy, scikit-network, infercnvpy and , hicat. hicat is used to annotate cell-type to collect reference cells for infercnv. All of them can be installed simply using pip command.

Contact

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