MACPET

DOI:10.18129/B9.bioc.MACPET

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, seeMACPET.

Model based analysis for paired-end data

Bioconductor version: 3.11

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

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 appropriateBioconductor release.

Documentation

查看文档的版本包age 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	1.8.0
In Bioconductor since	BioC 3.7 (R-3.5) (2.5 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
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Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	MACPET_1.8.0.tar.gz
Windows Binary	MACPET_1.8.0.zip(32- & 64-bit)
macOS 10.13 (High Sierra)	MACPET_1.8.0.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	//www.andersvercelli.com/packages/MACPET/
Package Downloads Report	Download Stats