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v1.0.0

TRANSIT MANUAL

  • TRANSIT Overview (4.0)
    • Typical Workflow
    • TPP (Transit Pre-Processor)
    • Combined_wig and Metadata Files
    • Genome Annotations (.prot_tables and .gff files)
    • GUI
    • Pre-Processing Tasks
    • Statistical Analysis Methods
    • Analyses for Tn5 Datasets
    • Results and Post-Processing
    • Command Line
    • Developers
    • References
  • Installation
    • Requirements
    • Python 3:
      • Additional Requirements: R (statistical analysis package)
    • Optional: Install BWA to use with TPP pre-processor
      • Linux & OSX Instructions
      • Windows Instructions
    • Upgrading
      • Method 1: Upgrading package installation
      • Method 2: Upgrading source installation
    • Installing wxPython
    • Troubleshooting
      • 1. No window appears when running in GUI mode.
      • 2. pip3: SystemError: Cannot compile ‘Python.h’.
      • 3. pip: “The following required packages can not be built: freetype,png,” etc.
      • 4. pip3: “No lapack/blas resources found”
      • 5. “resources.ContextualVersionConflict (six 1.5.2)…”
  • Running TRANSIT
    • GUI Mode
    • Command line Mode
  • Input Files for Transit
    • Combined_wig Files
    • Samples Metadata File
    • Genome Annotations (.prot_tables and .gff files)
  • Quality Control
    • QC Metrics Table
    • QC Plots
      • Figure 1: Read-Count Distribution
      • Figure 2: QQ-Plot of Read-Counts vs Geometric Distribution
      • Figure 3: Ranked plot of Read-Counts
    • Interpretation of Data Quality
    • What to do about Skewed Samples?
    • Beta-Geometric Correction

PRE-PROCESSING

  • Tnseq_stats
  • Scatterplot
    • Command Line Usage
    • Example Usage
    • GUI Mode
    • Runtime
  • Corrplot
    • Command Line Usage
    • GUI Mode
    • Runtime
  • Normalization
    • Command-line
    • GUI
    • Examples
  • Gene Means

ANALYSES of single conditions

  • Gumbel
    • How does it work?
    • Usage
    • Parameters
    • GUI Mode
    • Outputs and diagnostics
    • Run-time
  • HMM
    • How does it work?
    • Usage
    • Parameters
    • GUI Mode
    • Output and Diagnostics
      • Sites Output File:
      • Genes Output File:
    • Run-time
  • TTN-Fitness
    • Usage
    • GUI Mode
    • Volcano Plot
    • Output
      • Genes Output File:
      • Sites Output File:
    • Example of running the TTN-Fitness methodology on the sample glycerol data
    • Run-time

ANALYSES for pairwise comparisons

  • Resampling
    • How does it work?
    • Site-Restricted (S-R) Resampling
    • Usage
    • Parameters
    • Notes
    • Command Line Examples
    • Doing resampling with datasets from different libraries
    • Doing resampling between different strains
    • GUI Mode
    • Output and Diagnostics
    • Run-time
  • Mann-Whitney U-test (utest)
    • Usage
    • GUI Mode
    • Output
    • Runtime

ANALYSES for multiple conditions

  • Genetic Interactions
    • How does it work?
    • Statistical Significance
    • Usage
    • Example
    • Parameters
    • Gui Mode
    • Output and Diagnostics
    • Run-time
  • ANOVA
    • How does it work?
    • Example
    • Input files
    • Parameters
    • Output and Diagnostics
    • GUI Mode
    • Run-time
  • ZINB
    • How does it work?
    • Example
    • Input files
    • Parameters
    • Covariates and Interactions
    • Categorical vs Numeric Covariates
    • Statistical Significance - What the P-values Mean in the ZINB Output
    • GUI Mode
    • Output and Diagnostics
    • Run-time

POST-PROCESSING

  • Pathway Enrichment Analysis
    • Command Line Usage
    • Parameters
    • Auxilliary Pathway Files in Transit Data Directory
    • Current Recommendations
    • Examples
    • GUI Mode
    • Output and Diagnostics
    • Run-time
  • Heatmap
    • Command Line Usage:
    • GUI:

TPP Manual

  • TPP Overview
  • Installation
  • Running TPP
  • Mapping to Genomes with Multiple Contigs
  • 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
TRANSIT
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© Copyright 2015, Michael A. DeJesus & Thomas R. Ioerger.

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