AMiGA Anaylsis of Microbial Growth Assays

• Home
• Documentation
• Configuration
• Get Time at Threshold
• Estimate Confidence
• Code Vignette
• Compare Parameters
• Normalize Parameters
• Pool Replicates
• Detect Diauxie
• Command Line Interface
• Plot Heatmaps
• Test Hypotheses
• Subset Data
• Batch Analyze
• Fit Curves
• Summarize & Plot
• Prepare Metadata
• Prepare Data
• Install AMiGA
• Example Pipeline

Table of Contents

• Install Miniforge3
• Initialize mamba/conda
• Install AMiGA
• Test AMiGA
• Run AMiGA in the future

Install Miniforge3

Install Miniforge from here and follow the steps that are specific to your operating system.

Miniforge will allow you to use conda and mamba which are software that can help you install and run AMiGA on your machine. These software are environment management systems. In other words, they will let you create a unique environment on your machine to run AMiGA without affecting other environments that you create to run other software.

mamba is essentially a faster alternative to conda. We will use it below. If you prefer to use conda, then, you can simply replace all mamba instances below with conda.

Initialize mamba/conda

Open your Terminal and type

mamba init

This will simply tell your computer where to find mamba on your machine. Close the terminal.

Install AMiGA

Re-open the terminal and type

mamba create -n amiga-env bioconda::amiga

This will create an environment called amiga-env and install AMiGA inside this environment. This step will take a couple of minutes.

Test AMiGA

mamba activate amiga-env

This will activate the amiga-env environment. Now, your terminal should know where and how to run AMiGA. So, try to pull up the help menu.

amiga -v              # display AMiGA version numbers
amiga -h              # help menu
amiga summarize -h    # help menu for summarize command

You should get the following

usage: amiga <command> [<args>]

The most commonly used amiga commands are:
    summarize       Perform basic summary and plot curves
    fit             Fit growth curves
    normalize       Normalize growth parameters of fitted curves
    compare         Compare summary statistics for two growth curves
    test            Test a specific hypothesis
    heatmap         Plot a heatmap
    get_confidence  Compute confidence intervals for parameters or curves
    get_time        Get time at which growth reaches a certain value
    print_defaults  Shows the default values stored in libs/config.py

See `amiga <command> --help` for information on a specific command.
For full documentation, see https://firasmidani.github.io/amiga

positional arguments:
  command        Subcommand to run. See amiga --help for more details.

options:
  -h, --help     show this help message and exit
  -v, --version  Show version and exit.

Run AMiGA in the future

Open your Terminal, type mamba activate amiga-env, and you are ready to analyze your data.