MACPET

DOI: 10.18129/B9.bioc.MACPET    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see MACPET.

Model based analysis for paired-end data

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") 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	1.10.0
In Bioconductor since	BioC 3.7 (R-3.5) (3 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)
LinkingTo	Rcpp, bigmemory, BH
Suggests	ggplot2 (>= 3.2.0), igraph (>= 1.2.4.1), rmarkdown (>= 1.14), reshape2 (>= 1.4.3), BiocStyle(>= 2.13.2)
SystemRequirements	C++11
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Package Archives

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

Source Package	MACPET_1.10.0.tar.gz
Windows Binary	MACPET_1.10.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	MACPET_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MACPET
Source Repository (Developer Access)	git clone [email protected]:packages/MACPET
Package Short Url	https://bioconductor.org/packages/MACPET/
Package Downloads Report	Download Stats