DOI: 10.18129/B9.bioc.MACPET    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MACPET.

Model based analysis for paired-end data

Bioconductor version: 3.10

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.

Author: Ioannis Vardaxis

Maintainer: Ioannis Vardaxis <iova89 at>

Citation (from within R, enter citation("MACPET")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF   Reference Manual
Text   NEWS


biocViews Classification, Clustering, DNA3DStructure, HiC, PeakDetection, Software, StatisticalMethod
Version 1.6.0
In Bioconductor since BioC 3.7 (R-3.5) (2 years)
License GPL-3
Depends R (>= 3.6.1), InteractionSet(>= 1.13.0), bigmemory (>= 4.5.33), BH (>=, Rcpp (>= 1.0.1)
Imports intervals (>= 0.15.1), plyr (>= 1.8.4), Rsamtools(>= 2.1.3), stats (>= 3.6.1), utils (>= 3.6.1), methods (>= 3.6.1), GenomicRanges(>= 1.37.14), S4Vectors(>= 0.23.17), IRanges(>= 2.19.10), GenomeInfoDb(>= 1.21.1), gtools (>= 3.8.1), GenomicAlignments(>= 1.21.4), knitr (>= 1.23), rtracklayer(>= 1.45.1), BiocParallel(>= 1.19.0), Rbowtie(>= 1.25.0), GEOquery(>= 2.53.0), Biostrings(>= 2.53.2), ShortRead(>= 1.43.0), futile.logger (>= 1.4.3)
LinkingTo Rcpp, bigmemory, BH
Suggests ggplot2 (>= 3.2.0), igraph (>=, rmarkdown (>= 1.14), reshape2 (>= 1.4.3), BiocStyle(>= 2.13.2)
SystemRequirements C++11
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MACPET_1.6.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) MACPET_1.6.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: