Metadata-Version: 2.4
Name: transit1
Version: 3.3.12
Summary: TRANSIT is a tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.
Home-page: https://github.com/mad-lab/transit
Download-URL: https://github.com/mad-lab/transit
Author: Michael A. DeJesus
Author-email: mad@cs.tamu.edu
License: GNU GPL
Keywords: tnseq,analysis,biology,genome
Classifier: Development Status :: 5 - Production/Stable
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE.md
Requires-Dist: wheel
Requires-Dist: numpy~=1.16
Requires-Dist: scipy~=1.2
Requires-Dist: matplotlib~=3.0
Requires-Dist: pillow
Requires-Dist: scikit-learn
Requires-Dist: statsmodels~=0.9
Requires-Dist: pypubsub
Requires-Dist: wxPython
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: download-url
Dynamic: home-page
Dynamic: keywords
Dynamic: license
Dynamic: license-file
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# TRANSIT

[![Version](https://img.shields.io/github/tag/mad-lab/transit.svg)](https://github.com/mad-lab/transit)   [![Build Status](https://travis-ci.org/mad-lab/transit.svg?branch=master)](https://travis-ci.org/mad-lab/transit)   [![Documentation Status](https://readthedocs.org/projects/transit/badge/?version=latest)](http://transit.readthedocs.io/en/latest/?badge=latest)   [![Downloads](https://pepy.tech/badge/tnseq-transit)](https://pepy.tech/project/tnseq-transit)

=======

**NOTE: TRANSIT v3.0+ now requires python3.6+. If you want to use TRANSIT with python2, use version < 3.0.**

Welcome! This is the distribution for the TRANSIT and TPP tools developed by the [Ioerger Lab](http://orca2.tamu.edu/tom/iLab.html) at Texas A&M University.

TRANSIT is a tool for processing and statistical analysis of Tn-Seq data.
It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.

TRANSIT Home page: http://saclab.tamu.edu/essentiality/transit/index.html

TRANSIT Documentation: https://transit.readthedocs.io/en/stable/transit_overview.html

[Changelog](https://github.com/mad-lab/transit/blob/master/CHANGELOG.md)


## Features
TRANSIT offers a variety of features including:

-   More than **10 analysis methods**, including methods for determining **conditional essentiality** as well as **genetic interactions**.

-   Ability to analyze datasets from libraries constructed using  **himar1 or tn5 transposons**.

-   **TrackView** to help visualize read-counts across the genome.

-   Can **export datasets** into a variety of formats, including **IGV**.

-   Includes a **variety of normalization methods**.

-   **Quality Control** diagnostics, to idenfity poor quality datasets.

-   Ability to install as a **python package**, to import and use in your own personal scripts.



## Support

For any questions or comments, please contact Dr. Thomas Ioerger, ioerger@cs.tamu.edu.




## Instructions

For full instructions on how to install and run TRANSIT (and the optional pre-processor, TPP), please see the documentation included in this distribution ("src/pytransit/doc" folder) or visit the following web page:


https://transit.readthedocs.io/en/stable/


## Datasets

The TRANSIT distribution comes with some example .wig files in the data/ directory, as well as an example annotation file (.prot\_table format) in the genomes/ directory. Additional genomes may be found on the following website:

http://saclab.tamu.edu/essentiality/transit/genomes/


## Copyright Information

Source code for TRANSIT and TPP are available open source under the terms of the GNU General Public License (Version 3.0) as published by the Free Software Foundation. For more information on this license, please see the included LICENSE.md file or visit their website at:

http://www.gnu.org/licenses/gpl.html
