Metadata-Version: 2.4
Name: deeptools
Version: 4.0.0
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: numpy>=2.0
Requires-Dist: scipy>=1.13
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Requires-Dist: pybigwig>=0.3
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Requires-Dist: deeptoolsintervals>=0.1
Requires-Dist: maturin
Requires-Dist: flake8 ; extra == 'actions'
Requires-Dist: pytest ; extra == 'actions'
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Provides-Extra: actions
Provides-Extra: docs
License-File: LICENSE.txt
Summary: Useful tools for exploring deep sequencing data.
Author: Vivek Bhardwaj, Ward Deboutte, Lucille Delisle, Sarah Diehl, Galina Erikson, Friederike Dündar, Björn Grüning, Steffen Heyne, Fabian Kilpert, Wolfgang Maier, Thomas Manke, Saim Momin, Mohit Navander, Juan Perez Caballero, Fidel Ramirez, Adrian Salatino, Andreas S Richter, Devon P Ryan, Pavankumar Videm
Author-email: bioinfo-core@ie-freiburg.mpg.de
Requires-Python: >=3.12
Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
Project-URL: documentation, https://deeptools.readthedocs.io/en/latest/
Project-URL: homepage, https://pypi.python.org/pypi/deepTools/
Project-URL: repository, https://github.com/deeptools/deepTools

# deepTools
[![Documentation Status](https://readthedocs.org/projects/deeptools/badge/)](https://deeptools.readthedocs.io/) 
[![PyPI Version](https://img.shields.io/pypi/v/deeptools.svg?style=plastic)](https://pypi.org/project/deepTools/) 
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![planemo](https://github.com/deeptools/deepTools/actions/workflows/test_planemo.yml/badge.svg)


## User-friendly tools for exploring deep-sequencing data

deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating **normalized coverage files** in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready  **visualizations** to identify enrichments and for functional annotations of the genome.

For bug reports and feature requests please open an issue [on github](https://github.com/deeptools/deeptools).


### Citation:

Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. [deepTools2: a next generation web server for deep-sequencing data analysis.](https://nar.oxfordjournals.org/content/early/2016/04/12/nar.gkw257.abstract) Nucleic Acids Research. 2016 Apr 13:gkw257.

### Documentation:

Our [documentation](https://deeptools.readthedocs.io/) contains more details on the [individual tool scopes and usages](https://deeptools.readthedocs.io/en/latest/content/list_of_tools.html) and an [introduction to our deepTools Galaxy web server](https://deeptools.readthedocs.io/en/latest/content/help_galaxy_intro.html) including [step-by-step protocols](https://deeptools.readthedocs.io/en/latest/content/example_usage.html).

>Please see also the [FAQ](https://deeptools.readthedocs.io/en/latest/content/help_faq.html), which we update regularly.
Our [Gallery](https://deeptools.readthedocs.io/en/latest/content/example_gallery.html) may give you some more ideas about the scope of deepTools.


-------------------------------------------------------------------------------------------------------------------

### Installation

deepTools are available for:

* Command line usage (via pip / conda / github)
* Integration into Galaxy servers (via toolshed/API/web-browser)

There are many ways to install deepTools. More details can be found [here](https://deeptools.readthedocs.io/en/latest/content/installation.html).

In Brief, to install stable released version:

**Install via pip**

	$ pip install deeptools

**Install via conda**

	$ conda install -c conda-forge -c bioconda deeptools

**Install via uv / pipx / pixi**

	$ uv tool install deeptools
	$ pipx install deeptools
	$ pixi global install -c conda-forge -c bioconda deeptools

You can also install the latest development version (if you want to contribute or have the latest features).
The easiest way to do this is clone the repository and install with pixi (which will take care of the system dependencies via conda for you):

**Install by cloning the repository**

	$ git clone https://github.com/deeptools/deepTools
	$ cd deepTools
	$ pixi install

`pixi install` pins the whole build toolchain (Rust, `maturin`, `libclang`, HTSlib, ...) via
conda -- see [`pyproject.toml`](pyproject.toml)'s `[tool.pixi.dependencies]` for exactly what's
pinned. Building without pixi (via uv / pip / pipx) is possible too, but then you're responsible
for providing that same toolchain yourself; see the ["Building from
source"](https://deeptools.readthedocs.io/en/latest/content/installation.html#building-from-source)
section of the docs.

<a name="galaxy"/></a>
### Galaxy Installation

deepTools can be easily integrated into [Galaxy](https://galaxyproject.org). Please see the [installation instructions in our documentation](https://deeptools.readthedocs.io/en/latest/content/installation.html#galaxy-installation) for further details.

------------------------------------

[Documentation](https://deeptools.readthedocs.io/en/latest/index.html) | [FAQ](https://deeptools.readthedocs.io/en/latest/content/help_faq.html)

