Analysis Pipeline

Overview

There are three ways to run the MoSeq analysis pipeline, which are Jupyter notebooks and CLI. The Jupyter notebooks and CLI can be accessed through installation using Conda or the MoSeq2 Docker Image. The fosllowing sections contain instructions for Jupyter notebooks and CLI. You can find more information about the directory structure and intermediate yaml files in the analysis pipeline here.

Jupyter notebooks Instructions

MoSeq2 Extract Modeling Notebook

• MoSeq2 Extract Modeling Notebook Instructions
  • Project Setup
  • Raw Data Extraction
  • PCA
  • AR-HMM Modeling

MoSeq2 Analysis Visualization Notebook

• MoSeq2 Analysis Visualization Notebook Instructions
  • Project Setup
  • Compute Syllable Statistics
  • Interactive Syllable Labelling
  • Interactive Syllable Statistics Graphing
  • Syllable Transition Analysis

Flip Classifier Training Notebook

Command Line Interface Instructions

• Command Line Interface for Extraction and Modeling
  • Raw Data Extraction
  • PCA
  • AR-HMM Modeling
• Command Line Interface for Visualization
  • Get Best Fit Model
  • Further Extraction Diagnostics
  • Plot Syllable Statistics
  • Plot Syllable Transition Graphs

Which one do I use?

Below is a comparison of the two main MoSeq2 interfaces: the command-line interface, and the Jupyter notebook. You don't have to choose just one, as they can be used interchangeably.

Jupyter Notebook

Pros	Cons
Easy to use	Doesn't support automation
Shows both the code blocks and the output
Comes with interactive widgets to analyze model results

Command Line Interface (CLI)

Pros	Cons
Can be used in bash scripts flexibly for automation and parallelization	Can be confusing for users that have never used a CLI
	Limited visualization and interactive capabilities

If you are interested in using the CLI for extraction and modeling, but using the interactive widgets in the Jupyter notebooks to find parameters and analyze results interactively, you can find more information in extraction and modeling CLI documentation and the extraction and modeling or analysis notebook documentation.

Useful Resources

• Directory Structures and yaml Files in MoSeq Pipeline
  • Directory Structures
  • yaml Files in MoSeq Pipeline <- Google Colab>

Try Our Test Data

If you want to explore MoSeq functionalities, check out our test data.