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README.md

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Normalisr is written in Python3 and provides a command-line and a python functional interface. You can read more about Normalisr from our preprint (See [Citations](#citations)).
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## Install
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Normalisr is on PyPI (link TBA) and can be installed straightaway with pip (TB-uploaded): `pip install normalisr`. You can also install Normalisr from github (link TBD): `pip install`. Make sure you have added Normalisr's install path into PATH environment before using the command-line interface (See [FAQ](#faq)).
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## Installation
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Normalisr is on PyPI (link TBA) and can be installed straightaway with pip (TB-uploaded): `pip install normalisr`. You can also install Normalisr from github: `pip install git+https://github.com/lingfeiwang/normalisr.git`. Make sure you have added Normalisr's install path into PATH environment before using the command-line interface (See [FAQ](#faq)). Normalisr's installation should take less than a minute.
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There are more advanced installation methods but if you want that, most likely you already know how to do it ;). If not, give me a shout (See [Contact](#contact)).
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examples/README

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Here are several examples to demonstrate Normalisr's use. They are adapted for downsampled, small-scale demonstrations but can be applied on larger datasets straight-away. These examples are not meant to exactly reproduce results of the manuscript, although results can be highly similar, because some functions are missing (e.g. removal of cells from individuals with very few cells of the same cell type).
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Here are several examples to demonstrate Normalisr's use. They are adapted for downsampled, small-scale demonstrations but can be applied on larger datasets straight-away. These examples are not meant to exactly reproduce results of the manuscript, although results can be highly similar, because some functions are missing (e.g. removal of cells from individuals with very few cells of the same cell type). All of the examples should take less than 1 hour of running time on a normal computer (excluding data downloading and reformatting for Normalisr's input).
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See README.md in each example folder for more details.

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