SEMPLR

SEMPLR computes transcription factor binding affinity scores for genomic positions and genetic variants from SNP Effect Matrices (SEMs).

Key Features:

• SEM-based scoring: Scores are computed from SNP Effect Matrices (SEMs) produced by SEMpl.
• Pre-computed SEM library: 223 pre-computed SEMs are included with the package or custom sets can be provided.
• Enrichment testing: Enrichment can be tested among sets of genomic positions to determine if transcription factor binding events occur more often than expected.
• Allele-specific binding comparison: Comparing binding affinity scores between alleles can reveal differences in transcription factor binding with genetic variation.
• Visualization functions: Several visualization functions are included to view scores both on the motif and variant/position level.

Scientific Applications:

• Transcription factor binding prediction: Computing binding affinity scores for genomic positions and genetic variants to predict transcription factor binding events.
• Functional variant annotation: Comparing binding affinity scores between alleles to reveal differences in transcription factor binding associated with genetic variation.
• Binding enrichment analysis: Testing enrichment among sets of genomic positions to determine if transcription factor binding events occur more often than expected.

Methodology:

Scores are computed from SNP Effect Matrices (SEMs) produced by SEMpl.