semvec/pypi-packages huggingface dataset:
gadalang-lang 0.2a0
Collection of lang nodes for gada
Requires Python: >=3.7

# gadalang-lang

![PyPI - Python Version](https://img.shields.io/pypi/pyversions/gadalang-lang)
[![Python package](https://img.shields.io/github/workflow/status/gadalang/gadalang-lang/Python%20package)](https://github.com/gadalang/gadalang-lang/actions/workflows/python-package.yml)
[![Documentation Status](https://readthedocs.org/projects/gadalang-lang/badge/?version=latest)](https://gadalang-lang.readthedocs.io/en/latest/?badge=latest)
[![Codecov](https://img.shields.io/codecov/c/gh/gadalang/gadalang-lang?token=4CSJTL1ZML)](https://codecov.io/gh/gadalang/gadalang-lang)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/gadalang/gadalang-lang/issues)

Collection of [gada](https://github.com/gadalang/gada) nodes forming the core language.

## Install

Using pip:

```bash
$ pip3 install gadalang-lang
```

## Documentation

Build the doc with:

```bash
$ make html
```

You can find the latest documentation on [gadalang-lang.readthedocs.io](https://gadalang-lang.readthedocs.io/).

## Testing

The `test` directory contains many tests that you can run with:

```python
$ tox .
```

## License

Licensed under the [MIT](LICENSE) License.
epigeec-analysis 1.3.0
Analysis tools for epiGeEC
Requires Python: >=3.6.*

# epiGeEC Analysis #

The **epiGenomic Efficient Correlator (epiGeEC) Analysis** is a suite of tools to process, annotate and analyse correlation matrices generated by [**epiGeEC**](https://bitbucket.org/labjacquespe/epigeec/src/master/). A galaxy implementation featuring these tools and including thousands of pre-computed public epigenomic datasets is availalble at <http://epigeec.genap.ca/galaxy/>.

### Installation

Linux/x64 is the only OS currently supported, but it can work on any platform with python and pip installed.

#### Dependencies

You will need pip to install the python package, use the following command if not already installed

	sudo apt-get install python-pip

Pip will attempt to install all dependencies but most likely will fail

See documentation on how to install [pandas](https://github.com/svaksha/PyData-Workshop-Sprint/wiki/linux-install-pandas).

You might have more success with

	sudo apt-get install python-pandas

#### Install epiGeEC Analysis

    sudo pip install epigeec-analysis

### How To Use

This tool suite provide multiple analysis program.

For more info on each parameter use the help flag

	epigeec-analysis [tool] --help

#### Annotate matrix

Essentialy, this tool apply a hierachical cluster method on a correlation matrix to
regroup datasets in clusters associated with their metadatas.

![Hierarchical clustering](images/img5.jpg)



    epigeec-analysis annotate --pdf output.pdf --tsv output.tsv epiGeEC_Correlate.mat epiGeEC_Datasets.json assay cell_type timepoint

#### Evaluate clusters

    epigeec-analysis evaluate epiGeEC_Correlate.mat epiGeEC_Datasets.json -b assay cell_type timepoint -r assay cell_type timepoint > output.ari

### License

[GNU General Public License v3](LICENSE)