# NEET - Nanopore Error pattern Exploration Toolkit
The Nanopore Error pattern Exploration Toolkit (`NEET`) provides a range of functionalities that provide an easily accessible and interactive analysis approach for (systematic) base-calling errors in direct RNA nanopore sequencing data. The implemented modules include options for condensing, visualizing and differentiating error features contained in direct RNA sequencing data - including mismatch, deletion and insertion rates, among others.
## Installation
It is recommended to use Conda/Mamba and pip for installation:
```
conda create -y -n neet python==3.10 && conda activate neet
pip install neet-nanopore
neet --version
```
For more information and alternative installation approaches refer to the [Wiki](https://github.com/dietvin/neet/wiki/01-Installation).
## General usage
Once installed `NEET` can be accessed via the terminal:
```
neet --help
```
Individual modules can be accessed as follows:
```
neet [MODULE] --help
```
Available modules are:
- Pileup Extractor (`extractor`): Extract data from pileup files into feature tables
- Summary (`summmary`): Summarize and visualize feature tables
- Position-of-Interest Summary (`poisummary`): Summarize and visualize specific positions of interest
- Position-of-Interest View (`poiview`): Visualize positions of interest
- Position-of-Interest (`poicompare`): Statistically compare positions of interest
- Two-Sample Extractor (`extractdiff`): Identify and extract positions of increased error rates between two conditions
- Filter (`filter`): Filter feature tables by given features
- Bedops (`bedops`): Process and manipulate bed files
The modules are interconnected to provide different workflows for different scenarios. An overview of the main workflows is given below:
A detailled description of all available modules is provided in the [Wiki](https://github.com/dietvin/neet/wiki/02-Modules). The Wiki also provides [walkthroughs](https://github.com/dietvin/neet/wiki/03-Example-Workflows) for some possible use cases.
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"description": "# NEET - Nanopore Error pattern Exploration Toolkit\n\nThe Nanopore Error pattern Exploration Toolkit (`NEET`) provides a range of functionalities that provide an easily accessible and interactive analysis approach for (systematic) base-calling errors in direct RNA nanopore sequencing data. The implemented modules include options for condensing, visualizing and differentiating error features contained in direct RNA sequencing data - including mismatch, deletion and insertion rates, among others.\n\n## Installation\n\nIt is recommended to use Conda/Mamba and pip for installation:\n\n```\nconda create -y -n neet python==3.10 && conda activate neet\npip install neet-nanopore\nneet --version\n```\n\nFor more information and alternative installation approaches refer to the [Wiki](https://github.com/dietvin/neet/wiki/01-Installation).\n\n## General usage\n\nOnce installed `NEET` can be accessed via the terminal:\n\n```\nneet --help\n```\n\nIndividual modules can be accessed as follows:\n\n```\nneet [MODULE] --help\n```\n\nAvailable modules are:\n\n- Pileup Extractor (`extractor`): Extract data from pileup files into feature tables\n- Summary (`summmary`): Summarize and visualize feature tables\n- Position-of-Interest Summary (`poisummary`): Summarize and visualize specific positions of interest\n- Position-of-Interest View (`poiview`): Visualize positions of interest\n- Position-of-Interest (`poicompare`): Statistically compare positions of interest\n- Two-Sample Extractor (`extractdiff`): Identify and extract positions of increased error rates between two conditions\n- Filter (`filter`): Filter feature tables by given features\n- Bedops (`bedops`): Process and manipulate bed files\n The modules are interconnected to provide different workflows for different scenarios. An overview of the main workflows is given below:\n\n\n\nA detailled description of all available modules is provided in the [Wiki](https://github.com/dietvin/neet/wiki/02-Modules). The Wiki also provides [walkthroughs](https://github.com/dietvin/neet/wiki/03-Example-Workflows) for some possible use cases.\n",
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