MACPET

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: Release (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 hotmail.com>

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

Installation

To install this package, start R (version "4.2") 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

PDF   Reference Manual

Details

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 (>= 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
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
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: