MACPET

This package is for version 3.9 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: 3.9

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>

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

Installation

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


if (!require("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")
MACPET PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Clustering, DNA3DStructure, HiC, PeakDetection, Software, StatisticalMethod
Version 1.4.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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)
System Requirements C++11
URL
See More
Suggests ggplot2 (>= 3.1.0), igraph (>= 1.2.4), rmarkdown (>= 1.12), reshape2 (>= 1.4.3), BiocStyle(>= 2.11.0)
Linking To Rcpp, bigmemory, BH
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/MACPET/
Package Short Url https://bioconductor.org/packages/MACPET/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive