semvec/pypi-packages huggingface dataset:
masato 1.6.0
Modular Amplicon Sequencing Analysis TOokit
Requires Python: >=3.10

<h1>
  <img align="right" alt="Logo" width="120" height="120" src="logo.png">
  <br><br>
  Masato
</h1>

Masato is a modular amplicon sequencing analysis tookit. It highlights transparent and 
composible command line interface that helps users assemble and understand their pipeline.

NOTE: This package is renamed from [easy_amplicon](https://github.com/whatever60/easy_amplicon). The old repository has been archived.

## Try in Colab
[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1SPe_950g6cfB1PjDa8zKjgH4xgiiWQL_?usp=sharing)

Thie Colab notebook demonstrates basic usage of the package, example data included.


## Preprocessing

### Primers

- 16SV4 
  ```
  Fwd (2+19bp)
      GTGTGYCAGCMGCCGCGGTAA
      └┘└─────────────────┘
    Linker  16SV4-515F-Y

  Rev (2+20bp)
      CCGGACTACNVGGGTWTCTAAT
      └┘└──────────────────┘
    Linker  16SV4-515R-B
  ```
- 16SV3V4

- 16SV4V5
#### A note about the fesibility of pair merging
zonoopt 2.0.1
Python bindings for the ZonoOpt C++ library
Requires Python: >=3.9

# ZonoOpt

This C++ header library provides classes and tailored optimization routines for zonotopes, constrained zonotopes, and hybrid zonotopes. To use, `#include "ZonoOpt.hpp"`. All classes and methods are implemented using sparse linear algebra via the Eigen library. Generators may optionally have range [0,1] instead of [-1,1]. 

Python bindings can be installed from PyPI with `pip install zonoopt`. To build the bindings from source, use `pip install .`. Note that a C++ compiler is required to build from source, and the Eigen submodule must be checked out (can be accomplished by running `python3 update_submodules.py`).

More information about ZonoOpt can be found in the the following publication. Please cite this if you publish work based on ZonoOpt: 
**Robbins, J.A., Siefert, J.A., and Pangborn, H.C., "Sparsity-Promoting Reachability Analysis and Optimization of Constrained Zonotopes," 2025. [https://arxiv.org/abs/2504.03885](https://doi.org/10.48550/arXiv.2504.03885).**

Auto-generated API documentation is available below.

[C++ API](https://psu-PAC-Lab.github.io/ZonoOpt/C++/html/index.html)

[Python API](https://psu-PAC-Lab.github.io/ZonoOpt/python/build/html/index.html)

![image](images/mhe-traj.svg)
![image](images/reachability-traj.svg)
NodeGraphQtPy 0.6.38.7
NodeGraphQtPy is a fork of NodeGraphQt using QtPy
Requires Python: >3.7


# NOTICE: This project is deprecated.
The purpose of this project was to add support for QtPy and both PySide2 and PySide6. The original project NodeGraph has now switch to using QtPy and this project is now redundant.

# NodeGraphQtPy

This is a fork of the [NodeGraphQt](https://github.com/jchanvfx/NodeGraphQt) repo, using 
[QtPy](https://github.com/spyder-ide/qtpy) instead of [Qt.py](https://github.com/mottosso/Qt.py)
and with the goal of supporting both PySide2 and PySide6

#### The following README is from the original repo:

[![API Documentation](https://github.com/jchanvfx/NodeGraphQt/actions/workflows/sphinx_doc_build.yml/badge.svg)](https://github.com/jchanvfx/NodeGraphQt/actions/workflows/sphinx_doc_build.yml)
[![PyPI Package](https://github.com/jchanvfx/NodeGraphQt/actions/workflows/pypi_publish.yml/badge.svg)](https://github.com/jchanvfx/NodeGraphQt/actions/workflows/pypi_publish.yml)
![GitHub Repo stars](https://img.shields.io/github/stars/jchanvfx/NodeGraphQt?style=social)

<p align="center">
    <a href="https://jchanvfx.github.io/NodeGraphQt" target="_blank">
    <img src="https://raw.githubusercontent.com/jchanvfx/NodeGraphQt/main/docs/_images/logo.png" title="logo">
    </a>
</p>

NodeGraphQt is a node graph UI framework written in `PySide2` that can be re-implemented.

<img src="https://raw.githubusercontent.com/jchanvfx/NodeGraphQt/main/docs/_images/screenshot.png" width="100%" title="NodeGraphQt">

## Install

NodeGraphQt is available on The Python Package Index (PyPI) [here](https://pypi.org/project/NodeGraphQt) so it can be installed with:
```
pip install NodeGraphQt
```
or you can download previous versions from the [releases](https://github.com/jchanvfx/NodeGraphQt/releases) page.


## Documentation

<a href="https://jchanvfx.github.io/NodeGraphQt" target="_blank">https://jchanvfx.github.io/NodeGraphQt</a>

See the [basic_example.py](/examples/basic_example.py) script to get started or check out the API example overview 
<a href="https://jchanvfx.github.io/NodeGraphQt/api/examples/ex_overview.html#simple-example" target="_blank">here.</a>

## Vertical Layout

https://jchanvfx.github.io/NodeGraphQt/api/examples/ex_pipe.html#layout-direction

<img src="https://raw.githubusercontent.com/jchanvfx/NodeGraphQt/main/docs/_images/vertical_layout.png" width="800" title="Vertical Layout">

## Pipe Layout

https://jchanvfx.github.io/NodeGraphQt/api/examples/ex_pipe.html#layout-styles

<img src="https://raw.githubusercontent.com/jchanvfx/NodeGraphQt/main/docs/_images/pipe_layout_types.gif" width="600" title="Pipe Layout">

## Custom Widgets

https://jchanvfx.github.io/NodeGraphQt/api/custom_widgets.html

<img src="https://raw.githubusercontent.com/jchanvfx/NodeGraphQt/main/docs/_images/prop_bin.png" width="600" title="Properties Bin">

<img src="https://raw.githubusercontent.com/jchanvfx/NodeGraphQt/main/docs/_images/nodes_palette.png" width="450" title="Node Palette">