The following tutorials are designed to help you learn how to make the most out MotifCompendium. The first tutorial gives a minimal example of using the package. Subsequent tutorials aim to highlight additional features and utilities available in MotifCompendium. While it is sufficient to run MotifCompendium by simply following tutorial 1 exactly, it is highly recommended to run also run through tutorials 2-5 before using the package in order to most effectively use MotifCompendium. Tutorials 6-8 contain more advanced topics, and may be a useful reference depending on your use case.
When going through the tutorials, please read the text in between the code! The tutorials are supposed to represent a very thorough documentation of MotifCompendium functionality and usage suggestions. The text between the code is intended to help communicate usage suggestions and best practices.
- Tutorial 1 - Basic Usage: Gives a minimal example for using MotifCompendium.
- Tutorial 2 - The MotifCompendium Object: Describes how to interact with and manipulate MotifCompendium objects.
- Tutorial 3 - Motif Clustering: Describes options and best practices for clustering motifs.
- Tutorial 4 - Visualization: Describes options and best practices for visualizing motifs and motif clusters.
- Tutorial 5 - Motif Annotation: Describes options and best practices for automatically annotating motifs with MotifCompendium.
- Tutorial 6 - Motif Filtering: Describes options and best practices for filtering low quality motifs using entropy filters.
- Tutorial 7 - Additional Analyses: Gives examples of downstream analyses that can be performed using MotifCompendium, including exporting motifs to FiNeMo for hit calling and identifying celltype-specific motifs.
- Tutorial 8 - ENCODE Pipeline: The pipeline used to perform motif clustering on all ENCODE motifs. This tutorial is meant to demonstrate an extremely advanced use-case of MotifCompendium and should not be followed blindly.