MACPET

DOI: 10.18129/B9.bioc.MACPET    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MACPET.

Model based analysis for paired-end data

Bioconductor version: 3.9

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 <ioannis.vardaxis at ntnu.no>

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MACPET")

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

Documentation

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

browseVignettes("MACPET")

 

PDF	R Script	MACPET
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Clustering, DNA3DStructure, HiC, PeakDetection, Software, StatisticalMethod
Version	1.4.0
In Bioconductor since	BioC 3.7 (R-3.5) (1.5 years)
License	GPL-3
Depends	R (>= 3.6), InteractionSet(>= 1.11.2), bigmemory (>= 4.5.33), BH (>= 1.66.0.1), Rcpp (>= 1.0.1)
Imports	intervals (>= 0.15.1), plyr (>= 1.8.4), Rsamtools(>= 1.99.4), stats (>= 3.6.0), utils (>= 3.6.0), methods (>= 3.6.0), GenomicRanges(>= 1.35.1), S4Vectors(>= 0.21.21), IRanges(>= 2.17.4), GenomeInfoDb(>= 1.19.2), gtools (>= 3.8.1), GenomicAlignments(>= 1.19.1), knitr (>= 1.22), rtracklayer(>= 1.43.3), BiocParallel(>= 1.17.18), Rbowtie(>= 1.23.3), GEOquery(>= 2.51.5), Biostrings(>= 2.51.5), ShortRead(>= 1.41.0), futile.logger (>= 1.4.3)
LinkingTo	Rcpp, bigmemory, BH
Suggests	ggplot2 (>= 3.1.0), igraph (>= 1.2.4), rmarkdown (>= 1.12), reshape2 (>= 1.4.3), BiocStyle(>= 2.11.0)
SystemRequirements	C++11
Enhances
URL
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_1.4.0.tar.gz
Windows Binary	MACPET_1.4.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	MACPET_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MACPET
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MACPET
Package Short Url	https://bioconductor.org/packages/MACPET/
Package Downloads Report	Download Stats