TRANSIT - A Software Tool for Himar1 TnSeq Analysis
TnSeq has become a popular technique for determining the essentiality of genomic regions in bacterial organisms. Several methods have been developed to analyze the wealth of data that has been obtained through TnSeq experiments. We developed a tool for analyzing Himar1 TnSeq data called TRANSIT. TRA...
| Main Authors: | , , , , |
|---|---|
| Format: | Online |
| Language: | English |
| Published: |
Public Library of Science
2015
|
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4598096/ |
| id |
pubmed-4598096 |
|---|---|
| recordtype |
oai_dc |
| spelling |
pubmed-45980962015-10-20 TRANSIT - A Software Tool for Himar1 TnSeq Analysis DeJesus, Michael A. Ambadipudi, Chaitra Baker, Richard Sassetti, Christopher Ioerger, Thomas R. Research Article TnSeq has become a popular technique for determining the essentiality of genomic regions in bacterial organisms. Several methods have been developed to analyze the wealth of data that has been obtained through TnSeq experiments. We developed a tool for analyzing Himar1 TnSeq data called TRANSIT. TRANSIT provides a graphical interface to three different statistical methods for analyzing TnSeq data. These methods cover a variety of approaches capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. We demonstrate the utility of this software by analyzing TnSeq datasets of M. tuberculosis grown on glycerol and cholesterol. We show that TRANSIT can be used to discover genes which have been previously implicated for growth on these carbon sources. TRANSIT is written in Python, and thus can be run on Windows, OSX and Linux platforms. The source code is distributed under the GNU GPL v3 license and can be obtained from the following GitHub repository: https://github.com/mad-lab/transit Public Library of Science 2015-10-08 /pmc/articles/PMC4598096/ /pubmed/26447887 http://dx.doi.org/10.1371/journal.pcbi.1004401 Text en © 2015 DeJesus et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
DeJesus, Michael A. Ambadipudi, Chaitra Baker, Richard Sassetti, Christopher Ioerger, Thomas R. |
| spellingShingle |
DeJesus, Michael A. Ambadipudi, Chaitra Baker, Richard Sassetti, Christopher Ioerger, Thomas R. TRANSIT - A Software Tool for Himar1 TnSeq Analysis |
| author_facet |
DeJesus, Michael A. Ambadipudi, Chaitra Baker, Richard Sassetti, Christopher Ioerger, Thomas R. |
| author_sort |
DeJesus, Michael A. |
| title |
TRANSIT - A Software Tool for Himar1 TnSeq Analysis |
| title_short |
TRANSIT - A Software Tool for Himar1 TnSeq Analysis |
| title_full |
TRANSIT - A Software Tool for Himar1 TnSeq Analysis |
| title_fullStr |
TRANSIT - A Software Tool for Himar1 TnSeq Analysis |
| title_full_unstemmed |
TRANSIT - A Software Tool for Himar1 TnSeq Analysis |
| title_sort |
transit - a software tool for himar1 tnseq analysis |
| description |
TnSeq has become a popular technique for determining the essentiality of genomic regions in bacterial organisms. Several methods have been developed to analyze the wealth of data that has been obtained through TnSeq experiments. We developed a tool for analyzing Himar1 TnSeq data called TRANSIT. TRANSIT provides a graphical interface to three different statistical methods for analyzing TnSeq data. These methods cover a variety of approaches capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. We demonstrate the utility of this software by analyzing TnSeq datasets of M. tuberculosis grown on glycerol and cholesterol. We show that TRANSIT can be used to discover genes which have been previously implicated for growth on these carbon sources. TRANSIT is written in Python, and thus can be run on Windows, OSX and Linux platforms. The source code is distributed under the GNU GPL v3 license and can be obtained from the following GitHub repository: https://github.com/mad-lab/transit
|
| publisher |
Public Library of Science |
| publishDate |
2015 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4598096/ |
| _version_ |
1613485229145587712 |