Package: MACPET
Type: Package
Title: Model based analysis for paired-end data
Version: 1.0.0
Date: 2018-05-01
Author: Ioannis Vardaxis
Maintainer: Ioannis Vardaxis <ioannis.vardaxis@ntnu.no>
Description: The MACPET package can be used for binding site 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. MACPET is mainly written in C++, and it supports the BiocParallel package.
License: GPL-3
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.0.1
biocViews: Software, DNA3DStructure, PeakDetection, StatisticalMethod,
        Clustering, Classification, HiC
Depends: R (>= 3.5), InteractionSet (>= 1.7.6)
Imports: intervals (>= 0.15.1), plyr (>= 1.8.4), Rsamtools (>= 1.31.3),
        stats (>= 3.5.0), utils (>= 3.5.0), methods (>= 3.5.0),
        GenomicRanges (>= 1.31.20), S4Vectors (>= 0.17.32), IRanges (>=
        2.13.26), GenomeInfoDb (>= 1.15.5), gtools (>= 3.5.0),
        GenomicAlignments (>= 1.15.12), knitr (>= 1.19), Rcpp (>=
        0.12.15), rtracklayer (>= 1.39.9), BiocParallel (>= 1.13.1),
        Rbowtie (>= 1.19.1), GEOquery (>= 2.47.17), Biostrings (>=
        2.47.9), ShortRead (>= 1.37.1), rbamtools (>= 2.16.6),
        futile.logger (>= 1.4.3)
Suggests: ggplot2 (>= 2.2.1), igraph (>= 1.1.2), rmarkdown (>= 1.8),
        reshape2 (>= 1.4.3), BiocStyle (>= 2.7.8)
VignetteBuilder: knitr
LinkingTo: Rcpp
SystemRequirements: C++11
Collate: 'ALLData.R' 'AllClasses.R' 'AnalysisStatistics.R'
        'ConvertToPE_BAM.R' 'ConvertToPSelf-methods.R' 'InputChecks.R'
        'MACPETUlt.R' 'MACPET_pkg.R' 'PeaksToGRanges-methods.R'
        'PeaksToNarrowPeak-methods.R' 'RcppExports.R'
        'Stage_0_FilteringLinkersFunctions.R'
        'Stage_1_MappingFunctions.R'
        'Stage_2_PETClassificationFunctions.R'
        'Stage_3_PeakFinderFunctions.R' 'TagsToGInteractions-methods.R'
        'exportPeaks-methods.R' 'plot-methods.R' 'summary-methods.R'
NeedsCompilation: yes
Packaged: 2018-05-01 04:31:13 UTC; biocbuild
Built: R 3.5.0; i386-w64-mingw32; 2018-05-01 12:18:06 UTC; windows
Archs: i386, x64
