DOI: 10.18129/B9.bioc.MACPET  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see MACPET.

Model based analysis for paired-end data

Bioconductor version: 3.16

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")):


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biocViews Classification, Clustering, DNA3DStructure, HiC, PeakDetection, Software, StatisticalMethod
Version 1.18.0
In Bioconductor since BioC 3.7 (R-3.5) (5 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
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