TRANSIT
v2.0.1

TRANSIT Manual

  • Overview
  • Installation
  • Running TRANSIT
  • Analysis Methods

TRANSIT Tutorials

  • Tutorial: Essentiality Analysis in a Single Condition
  • Tutorial: Essentiality Analysis of the Entire Genome
  • Tutorial: Comparative Analysis - Glycerol vs Cholesterol
  • Tutorial: Export datasets

TPP Manual

  • Overview
  • Installation
  • Running TPP
  • Overview of Data Processing Procedure
  • Statistics

Code Documentation

  • transit package
TRANSIT
  • Docs »
  • Welcome to TRANSIT’s documentation!
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Welcome to TRANSIT’s documentation!¶

The main documentation for the site is organized into the following sections:

  • TRANSIT Manual
  • TRANSIT Tutorials
  • TPP Manual
  • Code Documentation

TRANSIT Manual¶

  • Overview
    • Tn5 Datasets
  • Installation
    • Requirements
    • Use as a Python Package
    • Detailed Instructions: Linux
    • Detailed Instructions: OSX
    • Detailed Instructions: Windows
  • Running TRANSIT
    • GUI Mode
    • Command line Mode
  • Analysis Methods
    • Gumbel
    • Tn5Gaps
    • HMM
    • Re-sampling
    • Normalization

TRANSIT Tutorials¶

  • 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

TPP Manual¶

  • Overview
  • Installation
  • Running TPP
  • Overview of Data Processing Procedure
  • Statistics

Code Documentation¶

  • transit package
    • Submodules
    • pytransit.norm_tools module
    • pytransit.stat_tools module
    • pytransit.tnseq_tools module
    • pytransit.transit_tools module
    • Module contents
  • Index
  • Module Index
  • Search Page
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© Copyright 2016, Michael A. DeJesus.

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