Package: MACPET
Type: Package
Title: Model based analysis for paired-end data
Version: 1.4.0
Date: 2019-03-30
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: 6.1.1
biocViews: Software, DNA3DStructure, PeakDetection, StatisticalMethod,
        Clustering, Classification, HiC
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)
Suggests: ggplot2 (>= 3.1.0), igraph (>= 1.2.4), rmarkdown (>= 1.12),
        reshape2 (>= 1.4.3), BiocStyle (>= 2.11.0)
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_9
git_last_commit: 74fa778
git_last_commit_date: 2019-05-02
Date/Publication: 2019-05-02
NeedsCompilation: yes
Packaged: 2019-05-03 02:55:24 UTC; biocbuild
Built: R 3.6.1; x86_64-apple-darwin13.4.0; 2019-07-29 08:44:41 UTC; unix
