Welcome to TRANSIT’s documentation!¶
Transit is python-based software for analyzing TnSeq data (sequencing data from transposon mutant libraries) to determine essentiality of bacterial genes under different conditions.
This page contains the documentation for TRANSIT. Below are a few quick links to some of the most important sections of the documentation, followed by a brief overview of TRANSIT’s features.
This documentation is for the original version of Transit. We recently released a new version of Transit called TRANSIT2 (re-implementation from scratch), which has most of the same TnSeq analytical methods, but it has an enhanced GUI. Nonetheless, this original version of TRANSIT is still being maintained for backwards-compatibility.
TRANSIT offers a variety of features including:
- More than 8 analysis methods, including methods for determining conditional essentiality as well as genetic interactions.
- Ability to analyze himar1 or tn5 transposons datasets.
- TrackView to help visualize read-counts accross 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.
- Mann-Whitney U-test (utest)
- Genetic Interactions
- Pathway Enrichment Analysis