MACPET

This package is for version 3.13 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: 3.13

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 hotmail.com>

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

Installation

To install this package, start R (version "4.1") 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 1.12.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3
Depends R (>= 3.6.1), InteractionSet(>= 1.13.0), bigmemory (>= 4.5.33), BH (>= 1.66.0.1), 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)
System Requirements C++11
URL
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Suggests ggplot2 (>= 3.2.0), igraph (>= 1.2.4.1), rmarkdown (>= 1.14), reshape2 (>= 1.4.3), BiocStyle(>= 2.13.2)
Linking To Rcpp, bigmemory, BH
Enhances
Depends On Me
Imports Me
Suggests Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MACPET_1.12.0.tar.gz
Windows Binary MACPET_1.12.0.zip
macOS 10.13 (High Sierra) MACPET_1.12.0.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 3.13 Source Archive