This work was part of the workshop on Single-Cell ATAC-seq Analysis organized by the Cell Discovery Network at Boston Children’s Hospital and Harvard Medical School, where I presented a session titled “Regulatory Motif Enrichment Analysis.”
In this tutorial, we’ll learn how to analyze DNA sequence motifs. Motifs are short DNA patterns that transcription factors bind to, and analyzing them can help us understand gene regulation.
We’ll explore two complementary ways to study motifs:
Motif enrichment in accessible regions – We'll identify which motifs are found more often in genomic regions (called peaks) that are more accessible in specific groups of cells. This helps us find transcription factors that might be active in those cells.
Differential motif activity analysis – We’ll also look at how the activity of specific motifs changes between different cell types or conditions. This method uses accessibility patterns to estimate how active certain transcription factors are in different groups of cells.
https://drive.google.com/file/d/1LfpMahzGBrT-VAprQ3pmIOOV6ZdmMqNQ/view?usp=sharing
and follow the motif_enrichment_analysis.ipynb