BioConductor
MACPET 1.0.0
Model based analysis for paired-end data
Released May 1, 2018 by Ioannis Vardaxis
Dependencies
GEOquery 2.48.0 ShortRead 1.38.0 rtracklayer 1.40.5 rbamtools 2.16.11 GenomeInfoDb 1.16.0 Rbowtie 1.20.0 gtools 3.8.1 futile.logger S4Vectors 0.18.3 BiocParallel 1.14.2 plyr 1.8.4 Rsamtools 1.32.3 InteractionSet 1.8.0 knitr 1.20 GenomicAlignments 1.16.0 Biostrings 2.48.0 intervals 0.15.1 GenomicRanges 1.32.6 IRanges 2.14.10 Rcpp
The MACPET package can be used for binding site 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. MACPET is mainly written in C++, and it supports the BiocParallel package.