FourCSeq

Package: FourCSeq
Type: Package
Title: Package analyse 4C sequencing data
Version: 1.6.2
Date: 2015-06-16
Author: Felix A. Klein, EMBL Heidelberg
Maintainer: Felix A. Klein <felix.klein@embl.de>
Depends: R (>= 3.0), GenomicRanges, ggplot2, DESeq2 (>= 1.9.11),
splines, methods, LSD
Imports: DESeq2, Biobase, Biostrings, GenomicRanges,
SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer,
fda, GenomicAlignments, gtools, Matrix
Suggests: BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene
VignetteBuilder: knitr
Description: FourCSeq is an R package dedicated to the analysis of
(multiplexed) 4C sequencing data. The package provides a
pipeline to detect specific interactions between DNA elements
and identify differential interactions between conditions. The
statistical analysis in R starts with individual bam files for
each sample as inputs. To obtain these files, the package
contains a python script (extdata/python/demultiplex.py) to
demultiplex libraries and trim off primer sequences. With a
standard alignment software the required bam files can be then
be generated.
License: GPL (>= 3)
biocViews: Software, Preprocessing, Sequencing
NeedsCompilation: no
Packaged: 2016-05-16 04:50:38 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'FourCSeq' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
** help
*** installing help indices
  converting help for package 'FourCSeq'
    finding HTML links ... done
    FourC                                   html  
    addFragments                            html  
    addPeaks                                html  
    addViewpointFrags                       html  
    combineFragEnds                         html  
    countFragmentOverlaps                   html  
    countFragmentOverlapsSecondCutter       html  
    distFitMonotone                         html  
    distFitMonotoneSymmetric                html  
    fc                                      html  
    fcf                                     html  
    findViewpointFragments                  html  
    getAllResults                           html  
    getDifferences                          html  
    getDistAroundVp                         html  
    getNormalizationFactors                 html  
    getReferenceSeq                         html  
    getZScores                              html  
    normalizeRPM                            html  
    plotDifferences                         html  
    plotFits                                html  
    plotNormalizationFactors                html  
    plotScatter                             html  
    plotZScores                             html  
    smoothCounts                            html  
    smoothHitPerCent                        html  
    writeTrackFiles                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
* DONE (FourCSeq)
Making 'packages.html' ... done