CODEX

Package: CODEX
Type: Package
Title: A Normalization and Copy Number Variation Detection Method for
Whole Exome Sequencing
Version: 1.4.0
Author: Yuchao Jiang, Nancy R. Zhang
Maintainer: Yuchao Jiang <yuchaoj@wharton.upenn.edu>
Description: A normalization and copy number variation calling procedure for
whole exome DNA sequencing data. CODEX relies on the availability of
multiple samples processed using the same sequencing pipeline for
normalization, and does not require matched controls. The normalization
model in CODEX includes terms that specifically remove biases due to GC
content, exon length and targeting and amplification efficiency, and latent
systemic artifacts. CODEX also includes a Poisson likelihood-based recursive
segmentation procedure that explicitly models the count-based exome
sequencing data.
License: GPL-2
Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb,
BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings
Suggests: WES.1KG.WUGSC
biocViews: ExomeSeq, Normalization, QualityControl, CopyNumberVariation
LazyData: yes
NeedsCompilation: no
Packaged: 2016-05-04 06:01:34 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'CODEX' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CODEX'
    finding HTML links ... done
    CODEX-package                           html  
    bambedObjDemo                           html  
    choiceofK                               html  
    coverageObjDemo                         html  
    gcDemo                                  html  
    getbambed                               html  
    getcoverage                             html  
    getgc                                   html  
    getmapp                                 html  
    mappDemo                                html  
    mapp_ref                                html  
    mappability                             html  
    normObjDemo                             html  
    normalize                               html  
    normalize2                              html  
    qc                                      html  
    qcObjDemo                               html  
    segment                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CODEX)
Making 'packages.html' ... done