Model based analysis for paired-end data
The MACPET package can be used for complete interaction analysis for ChIA-PET data. MACPET reads ChIA-PET data in BAM or SAM format and separates the data into Self-ligated, Intra- and Inter-chromosomal PETs. Furthermore, MACPET breaks the genome into regions and applies 2D mixture models for identifying candidate peaks/binding sites using skewed generalized students-t distributions (SGT). It then uses a local poisson model for finding significant binding sites. Finally it runs an additive interaction-analysis model for calling for significant interactions between those peaks. MACPET is mainly written in C++, and it also supports the BiocParallel package.