MINORg

Source code

https://github.com/rlrq/MINORg

Module contents

• 1. Installation
  • 1.1. Running in Docker
  • 1.2. Note for Windows users
  • 1.3. Dependencies
  • 1.4. Install MINORg
• 2. Overview
  • 2.1. Command line
  • 2.2. Python package
• 3. Configuration
  • 3.1. config file
  • 3.2. Alias lookups
• 4. Tutorial (Docker)
  • 4.1. Running MINORg image as container
  • 4.2. Preparing files
  • 4.3. Importing files
  • 4.4. Running MINORg
  • 4.5. Exporting output files
  • 4.6. Exiting the container
  • 4.7. Reusing the container
  • 4.8. Removing the container
  • 4.9. Docker docs
• 5. Tutorial (Command line)
  • 5.1. Setting up the tutorial
  • 5.2. IMPT: Note on executables
  • 5.3. Defining target sequences
  • 5.4. Defining gRNA
  • 5.5. Filtering gRNA
  • 5.6. Generating minimum gRNA set(s)
  • 5.7. Subcommands
  • 5.8. Defining reference genomes
  • 5.9. Multithreading
• 6. Tutorial (Python)
  • 6.1. Setting up the tutorial
  • 6.2. Getting started
  • 6.3. IMPT: Note on executables
  • 6.4. Defining target sequences
  • 6.5. Defining gRNA
  • 6.6. Filtering gRNA
  • 6.7. Generating minimum gRNA set(s)
  • 6.8. Subcommands
  • 6.9. Defining reference genomes
  • 6.10. Multithreading
  • 6.11. Differences between CLI and Python versions
• 7. Parameters
  • 7.1. CLI vs Python
  • 7.2. Parameter types
  • 7.3. Parameter descriptions
• 8. Output
  • 8.1. Directory structure
  • 8.2. Output files
• 9. Algorithms
  • 9.1. Non-reference homologue inference
  • 9.2. Off-target assessment
  • 9.3. Within-feature inference
  • 9.4. Minimum set generation
• 10. Examples
  • 10.1. Example 1
  • 10.2. Example 2

Documentation

• API documentation
  • minorg.MINORg module
  • minorg.MINORgCLI module
  • minorg.annotation module
  • minorg.blast module
  • minorg.console module
  • minorg.constants module
  • minorg.display module
  • minorg.dynamic_logger module
  • minorg.extend_reference module
  • minorg.extract_homologue module
  • minorg.fasta module
  • minorg.filter_grna module
  • minorg.functions module
  • minorg.generate_grna module
  • minorg.grna module
  • minorg.index module
  • minorg.log module
  • minorg.main module
  • minorg.mafftcommandline_add module
  • minorg.minimum_set module
  • minorg.minweight_sc module
  • minorg.pam module
  • minorg.parse_config module
  • minorg.reference module