SomatiCA

Package: SomatiCA
Type: Package
Title: SomatiCA: identifying, characterizing, and quantifying somatic
copy number aberrations from cancer genome sequencing
Version: 2.2.0
Date: 2016-04-15
Author: Mengjie Chen <mengjie.chen@yale.edu>, Hongyu Zhao
<hongyu.zhao@yale.edu>
Maintainer: Mengjie Chen <mengjie.chen@yale.edu>
Imports: foreach, lars, sn, DNAcopy, methods, rebmix, GenomicRanges,
IRanges
Depends: R (>= 2.14.0), lars, DNAcopy, foreach, methods, rebmix,
GenomicRanges, IRanges, doParallel
Enhances: sn, SomatiCAData
Description: SomatiCA is a software suite that is capable of
identifying, characterizing, and quantifying somatic CNAs from
cancer genome sequencing. First, it uses read depths and lesser
allele frequencies (LAF) from mapped short sequence reads to
segment the genome and identify candidate CNAs. Second,
SomatiCA estimates the admixture rate from the relative
copy-number profile of tumor-normal pair by a Bayesian finite
mixture model. Third, SomatiCA quantifies absolute somatic
copy-number and subclonality for each genomic segment to guide
its characterization. Results from SomatiCA can be further
integrated with single nucleotide variations (SNVs) to get a
better understanding of the tumor evolution.
License: GPL (>=2)
biocViews: Sequencing, CopyNumberVariation
PackageStatus: Deprecated
NeedsCompilation: no
Packaged: 2016-05-04 04:51:18 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'SomatiCA' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'sn::coef' by 'rebmix::coef' when loading 'SomatiCA'
Warning: replacing previous import 'rebmix::split' by 'GenomicRanges::split' when loading 'SomatiCA'
Warning: replacing previous import 'sn::sd' by 'IRanges::sd' when loading 'SomatiCA'
** help
*** installing help indices
  converting help for package 'SomatiCA'
    finding HTML links ... done
    GCbiasRemoval                           html  
    GCcontent                               html  
    GCcount                                 html  
    MergeSegment                            html  
    SomatiCA-package                        html  
    SomatiCAFormat-methods                  html  
    SomatiCAUsersGuide                      html  
    SomatiCApipe                            html  
    admixtureRate                           html  
    collapse                                html  
    copynumberCorrected                     html  
    denoise                                 html  
    larsCBSsegment                          html  
    plotSegment                             html  
    plotSubclonality                        html  
    refineSegment                           html  
    segmentGCbiasRemoval                    html  
    segwithratio                            html  
    somaticRatio                            html  
    subclonality                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'sn::coef' by 'rebmix::coef' when loading 'SomatiCA'
Warning: replacing previous import 'rebmix::split' by 'GenomicRanges::split' when loading 'SomatiCA'
Warning: replacing previous import 'sn::sd' by 'IRanges::sd' when loading 'SomatiCA'
Warning: Package 'SomatiCA' is deprecated and will be removed from Bioconductor
  version 3.3
* DONE (SomatiCA)
Making 'packages.html' ... done