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.

Package details

AuthorIoannis Vardaxis
Bioconductor views Classification Clustering DNA3DStructure HiC PeakDetection Software StatisticalMethod
MaintainerIoannis Vardaxis <[email protected]>
LicenseGPL-3
Version1.4.0
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MACPET")

Try the MACPET package in your browser

Any scripts or data that you put into this service are public.

MACPET documentation built on May 6, 2019, 3:31 a.m.