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README.md

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![PyPI](https://img.shields.io/pypi/v/sclitr)
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![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)
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scLiTr is a Python package for analysis of lineage tracing coupled with single-cell RNA-Seq.
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clone2vec is a Python package for analysis of lineage tracing coupled with single-cell RNA-Seq.
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The main key of the package are clonal embeddings — vector representations of the whole clones
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in low dimensional space (clone2vec). These representations is a dropout-robust and cluster-free
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in low dimensional space. These representations is a dropout-robust and cluster-free
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way of representation of heterogeneity within clonal behaviour for cell type tree-free hypothesis
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generation regarding cells' multipotency.
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## Installation
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scLiTr might be installed via `pip` (takes 1-2 minutes on Google Colab):
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clone2vec might be installed via `pip` (takes 1-2 minutes on Google Colab):
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```bash
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pip install sclitr
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```
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or the latest development version can be installed from GitHub using:
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```bash
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pip install git+https://github.com/kharchenkolab/scLiTr
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pip install git+https://github.com/kharchenkolab/clone2vec
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```
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## System requirements
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`scLiTr` requires Python 3.8 or later with packages listed in [setup.cfg](setup.cfg) file. The package was successfully tested
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`clone2vec` requires Python 3.8 or later with packages listed in [setup.cfg](setup.cfg) file. The package was successfully tested
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on the following systems:
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* macOS Sonoma 14.5 (Apple M1 Chip @ 3.20GHz × 8, 16GB RAM) — *MacBook Air M1*,

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