SEMPLR
SEMPLR computes transcription factor binding affinity scores for genomic positions and genetic variants. Scores are computed from SNP Effect Matrices (SEMs) produced by SEMpl. 223 pre-computed SEMs are included with the package or custom sets can be provided. Enrichment can be tested among sets of genomic positions to determine if transcription factor binding events occur more often than expected. Comparing binding affinity scores between alleles can reveal differences in transcription factor binding with genetic variation. This package also includes several visualization functions to view scores both on the motif and variant/position level.
README
SEMPLR Overview SEMPLR (SNP Effect Matrix Pipeline in R) is an R package that predicts transcription factor (TF) binding. SEMPLR can be used to predict binding affinity of TFs at genomic loci or predict the affect of genetic variation on TF binding. SEMPLR scores genomic regions or sequences of interest against SNP Effect Matrices (SEMs). SEMs are position x nucleotide matrix, generated by integrating information from position weighted matrices (PWMs), ChIP-seq, and DNase-seq data. This…
- Repository
- github.com/grkenney/semplr
Source attribution
- GitHub — github.com/grkenney/semplr
- Bioconductor — SEMPLR
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