Welcome to TRANSITS’s documentation!

TRANSIT Manual

• Overview
• Installation
  • Requirements
  • Detailed Instructions: Linux
  • Detailed Instructions: OSX
  • Detailed Instructions: Windows
• Running TRANSIT
  • GUI Mode
  • Command line Mode
• Analysis Methods
  • Gumbel
  • Tn Gaps
  • HMM
  • Re-sampling
• Tutorial: Essentiality Analysis in a Single Condition
  • Run TRANSIT
  • Adding the annotation file
  • Adding the control datasets
  • Visualizing read counts
  • Scatter plot
  • Essentiality analysis with the Gumbel method
• Tutorial: Essentiality Analysis of the Entire Genome
  • Run TRANSIT
  • Adding the annotation file
  • Adding the control datasets
  • Visualizing read counts
  • Scatter plot
  • Essentiality analysis with the HMM method
• Tutorial: Comparative Analysis - Glycerol vs Cholesterol
  • Run TRANSIT
  • Adding the annotation file
  • Adding the control datasets
  • Visualizing read counts
  • Scatter plot
• Tutorial: Export datasets
  • Adding the annotation file
  • Add .wig datasets
  • Export to IGV

Code Documentation

• transit Package
  • transit Package
  • draw_trash Module
  • fileDisplay Module
  • images Module
  • norm_tools Module
  • qcDisplay Module
  • stat_tools Module
  • tnseq_tools Module
  • transit_gui Module
  • transit_tools Module
  • trash Module
  • view_trash Module
  • Subpackages

• Index
• Module Index
• Search Page