bioc-issue-bot
commented
7 years ago Hi @IoannisVardaxis
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: MACPET
Type: Package
Title: Model based analysis for ChIA-PET data
Version: 0.99.0
Date: 2017-25-10
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, Bayesian, Clustering, Classification, HiC
Depends: R (>= 3.4.2), InteractionSet (>= 1.4.0)
Imports: intervals (>= 0.15.1), plyr (>= 1.8.4), Rsamtools (>= 1.28.0), stats (>= 3.4.2), utils (>= 3.4.2), methods (>= 3.4.2), GenomicRanges (>= 1.28.6), S4Vectors (>= 0.14.7), IRanges (>= 2.10.5), GenomeInfoDb (>= 1.12.3), gtools (>= 3.5.0), GenomicAlignments (>= 1.12.2), BSgenome (>= 1.44.2), knitr (>= 1.17), Rcpp (>= 0.12.13), rtracklayer (>= 1.36.6), BiocParallel (>= 1.10.1)
Suggests: ggplot2 (>= 2.2.1), igraph (>= 1.1.2), rmarkdown (>= 1.6.0.9004), reshape2 (>= 1.4.2), BiocStyle (>= 2.4.1)
VignetteBuilder: knitr
RdMacros: Rdpack
LinkingTo: Rcpp
Collate:
'ALLData.R'
'AllClasses.R'
'AnalysisStatistics.R'
'ConvertToPSelf-methods.R'
'InputChecks.R'
'MACPET_pkg.R'
'PeakCallerUlt.R'
'PeaksToGRanges-methods.R'
'PeaksToNarrowPeak-methods.R'
'RcppExports.R'
'Stage_0_PETClassificationFunctions.R'
'Stage_1_PeakFinderFunctions_R.R'
'TagsToGInteractions-methods.R'
'exportPeaks-methods.R'
'plot-methods.R'
'summary-methods.R'
IoannisVardaxis
nturaga
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