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("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 | R Script | |
| Reference Manual | ||
| 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 |