TRANSIT

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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 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

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