Overview: permseq is a specialized R package designed for analyzing protein-DNA interactions in highly repetitive regions of the genome. By implementing a prior-enhanced read mapping strategy, permseq enables accurate identification of binding sites in traditionally challenging genomic regions.
Key Features:
Prior-Enhanced Mapping:
- Integration of prior knowledge
- Enhanced repetitive region analysis
- Improved mapping accuracy
- Multi-mapping read resolution
Comprehensive Analysis Pipeline:
- ChIP-seq data processing
- Binding site identification
- Signal enrichment analysis
- Peak calling optimization
Statistical Framework:
- Robust statistical modeling
- Uncertainty quantification
- Quality score assessment
- Significance evaluation
User-Friendly Implementation:
- Simple R interface
- Extensive documentation
- Example datasets
- Step-by-step tutorials
Applications: permseq has been successfully applied to:
- Map protein binding in repetitive regions
- Analyze complex genomic architectures
- Study transcription factor binding
- Identify novel regulatory elements
- Characterize chromatin states
The package is implemented in R with Perl support for data processing, providing comprehensive documentation and tutorials to support researchers in the fields of genomics and epigenetics.
Ye Zheng
Assistant Professor, PI
Research interests include Multi-omics, Statistical Modeling, Computational Biology, Cancer Research