| Name | inferploidy JSON |
| Version |
0.3.3
JSON |
| download |
| home_page | https://github.com/combio-dku |
| Summary | Tookits for Tumor cell identification in single-cell RNA-seq data |
| upload_time | 2025-07-15 05:09:01 |
| maintainer | None |
| docs_url | None |
| author | Seokhyun Yoon |
| requires_python | None |
| license | MIT License
Copyright (c) 2024 Machine Learning & Bioinformatics Lab.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
|
| keywords |
single-cell omics
bioinformatics
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
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# 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](https://github.com/icbi-lab/infercnvpy) .
## Cite InferPloidy
- "InferPloidy: A fast ploidy inference tool accurately classifies cells with abnormal CNVs in large single-cell RNA-seq datasets", available at [bioRxiv](https://doi.org/10.1101/2025.03.13.643178)
<div align="center">
<img src="https://github.com/combio-dku/inferploidy/blob/main/images/inferploidy.png" style="width:80%;"/>
</div>
## 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
Send email to syoon@dku.edu for any inquiry on the usages.
Raw data
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