motifTestR

motifTestR performs statistical tests for over-representation of sequence motifs represented as PWMs in sequence data, including tests for positional features within motif sets.

Key Features:

• Motif over-representation testing: Tests sequences for over-representation of a set of input motifs provided as PWMs.
• Positional feature analysis: Tests for positional features within the set of motifs.
• Multiple statistical approaches: Enrichment analysis can be undertaken using multiple statistical approaches.
• Data preparation functions: Contains core functions to prepare data for analysis.
• Result visualization: Contains core functions to visualise results.

Scientific Applications:

• Binding motif enrichment analysis: Identifies over-represented transcription factor binding motifs or other regulatory motifs in sequence sets.
• Positional motif analysis: Investigates spatial distribution and positional preferences of motifs within sequences.

Methodology:

motifTestR takes a set of sequence motifs as PWMs and tests a set of sequences for over-representation of these motifs, with enrichment analysis using multiple statistical approaches.