Package: MACPET
Type: Package
Title: Model based analysis for paired-end data
Version: 1.2.0
Date: 2018-05-01
Author: Ioannis Vardaxis
Maintainer: Ioannis Vardaxis <ioannis.vardaxis@ntnu.no>
Description: 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.
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 (>= 1.8.0), bigmemory (>= 4.5.33),
        BH (>= 1.66.0.1), Rcpp (>= 0.12.17)
Imports: intervals (>= 0.15.1), plyr (>= 1.8.4), Rsamtools (>= 1.32.0),
        stats (>= 3.5.0), utils (>= 3.5.0), methods (>= 3.5.0),
        GenomicRanges (>= 1.32.3), S4Vectors (>= 0.18.3), IRanges (>=
        2.14.10), GenomeInfoDb (>= 1.16.0), gtools (>= 3.8.1),
        GenomicAlignments (>= 1.16.0), knitr (>= 1.20), rtracklayer (>=
        1.40.3), BiocParallel (>= 1.14.1), Rbowtie (>= 1.20.0),
        GEOquery (>= 2.48.0), Biostrings (>= 2.48.0), ShortRead (>=
        1.38.0), rbamtools (>= 2.16.11), futile.logger (>= 1.4.3)
Suggests: ggplot2 (>= 3.0.0), igraph (>= 1.2.1), rmarkdown (>= 1.10),
        reshape2 (>= 1.4.3), BiocStyle (>= 2.8.2)
VignetteBuilder: knitr
LinkingTo: Rcpp, bigmemory, BH
SystemRequirements: C++11
Collate: 'ALLData.R' 'AllClasses.R' 'AnalysisStatistics.R'
        'ConvertToPE_BAM.R' 'ConvertToPSelf-methods.R'
        'GetShortestPath-methods.R' 'GetSignInteractions-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'
        'Stage_4_InteractionsFunctions.R'
        'TagsToGInteractions-methods.R' 'exportPeaks-methods.R'
        'plot-methods.R' 'summary-methods.R'
git_url: https://git.bioconductor.org/packages/MACPET
git_branch: RELEASE_3_8
git_last_commit: 7c55f69
git_last_commit_date: 2018-10-30
Date/Publication: 2018-10-30
NeedsCompilation: yes
Packaged: 2018-10-31 02:13:53 UTC; biocbuild
Built: R 3.5.1; x86_64-apple-darwin15.6.0; 2018-10-31 09:07:42 UTC; unix
