IoannisVardaxis/MACPET: 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.

Getting started

Package details

AuthorIoannis Vardaxis
Bioconductor views Classification Clustering DNA3DStructure HiC PeakDetection Software StatisticalMethod
MaintainerIoannis Vardaxis <>
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
IoannisVardaxis/MACPET documentation built on Aug. 9, 2019, 12:11 p.m.