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.
install-linkmanual-linktutorial-linktpp-linkcode-link- PDF manual with overview of analysis methods in Transit
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.
transit_overview transit_install transit_running transit_features
method_gumbel method_griffin method_tn5gaps method_HMM method_resampling method_Utest method_GI method_anova method_zinb method_normalization method_pathway_enrichment method_tnseq_stats method_corrplot method_heatmap method_ttnfitness
transit_essentiality_tutorial transit_genome_tutorial transit_comparative_tutorial transit_interactions_tutorial transit_normalization_tutorial transit_export_tutorial transit_console_cheatsheet
tpp.rst
transit
genindexmodindexsearch
For any questions or comments, please contact Dr. Thomas Ioerger, ioerger@cs.tamu.edu.