ArticlePLoS computational biology2015
TRANSIT--A Software Tool for Himar1 TnSeq Analysis.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 180 papers.
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180 citing papers in PubMed.
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- Mycobacterium tuberculosis long-chain fatty acid resistome reveals universal stress protein TB15.3 as essential for infection.Communications biology · 2026Article
- Non-canonical peptidoglycan cross-linking is essential forbioRxiv : the preprint server for biology · 2026Article
- A murine model of adult gastrointestinal colonization by Group BInfection and immunity · 2026Article
- Global genetic rewiring during compensatory evolution in the yeast polarity network.EMBO reports · 2026Article
- ConNIS and labeling instability: New statistical methods for improving the detection of essential genes in TraDIS libraries.PLoS computational biology · 2026Article
120 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
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.
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