Last data update: 2014.03.03


Package: AneuFinder
Type: Package
Title: Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Version: 1.0.3
Date: 2016-05
Author: Aaron Taudt, Bjorn Bakker, David Porubsky
Maintainer: Aaron Taudt <>
Description: This package implements functions for CNV calling, plotting, export
and analysis from whole-genome single cell sequencing data.
Depends: R (>= 3.3.0), GenomicRanges, cowplot, AneuFinderData
Imports: utils, grDevices, graphics, stats, foreach, doParallel,
BiocGenerics, S4Vectors, GenomeInfoDb, IRanges, Rsamtools,
Biostrings, GenomicAlignments, preseqR, ggplot2, reshape2,
ggdendro, ReorderCluster, mclust
Suggests: knitr, testthat, BSgenome.Hsapiens.UCSC.hg19,
License: Artistic-2.0
LazyLoad: yes
VignetteBuilder: knitr
Packaged: 2016-06-02 06:07:27 UTC; biocbuild
biocViews: Software, CopyNumberVariation, GenomicVariation,
HiddenMarkovModel, WholeGenome
RoxygenNote: 5.0.1
NeedsCompilation: yes

● BiocViews: CopyNumberVariation, GenomicVariation, HiddenMarkovModel, Software, WholeGenome
24 images, 50 functions, 0 datasets
● Reverse Depends: 0

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'AneuFinder' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c R_interface.cpp -o R_interface.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c densities.cpp -o densities.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.cpp -o init.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c loghmm.cpp -o loghmm.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c scalehmm.cpp -o scalehmm.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c utility.cpp -o utility.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/AneuFinder/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'AneuFinder'
    finding HTML links ... done
    AneuFinder-package                      html  
    Aneufinder                              html  
    finding level-2 HTML links ... done

    aneuBiHMM                               html  
    aneuHMM                                 html  
    bam2GRanges                             html  
Rd warning: /tmp/RtmpFVoyN0/R.INSTALL67b53809f099/AneuFinder/man/bam2GRanges.Rd:28: missing file link 'scanBamWhat'
    bed2GRanges                             html  
    binReads                                html  
Rd warning: /tmp/RtmpFVoyN0/R.INSTALL67b53809f099/AneuFinder/man/binReads.Rd:74: missing file link 'countOverlaps'                             html  
    binning                                 html  
    bivariate.findCNVs                      html  
    blacklist                               html  
    clusterByQuality                        html  
    collapseBins                            html  
    colors                                  html  
    correctGC                               html  
    correctMappability                      html  
    deltaWCalculator                        html  
    estimateComplexity                      html  
    export                                  html  
    filterSegments                          html  
    findCNVs                                html  
    findSCEs                                html  
    fixedWidthBins                          html  
    getSCEcoordinates                       html  
    getSegments                             html  
    heatmapAneuploidies                     html  
    heatmapGenomewide                       html  
    hotspotter                              html  
    importBed                               html  
    initializeStates                        html  
    karyotypeMeasures                       html  
    loadGRangesFromFiles                    html  
    loadHmmsFromFiles                       html  
    plot.GRanges                            html  
    plot.aneuBiHMM                          html  
    plot.aneuHMM                            html  
    plot.character                          html  
    plotBinnedDataHistogram                 html  
    plotKaryogram                           html  
    plotProfile                             html  
    plotUnivariateHistogram                 html  
    qualityControl                          html  
    readConfig                              html  
    simulateReads                           html  
Rd warning: /tmp/RtmpFVoyN0/R.INSTALL67b53809f099/AneuFinder/man/simulateReads.Rd:27: missing file link 'BSgenome'
Rd warning: /tmp/RtmpFVoyN0/R.INSTALL67b53809f099/AneuFinder/man/simulateReads.Rd:11: missing file link 'BSgenome'
    subsetByCNVprofile                      html  
    transCoord                              html  
    univariate.findCNVs                     html  
    variableWidthBins                       html  
    writeConfig                             html  
    zinbinom                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AneuFinder)
Making 'packages.html' ... done