MSIseq

Package: MSIseq
Maintainer: Mini Huang <mini.huang@nus.edu.sg>
License: GPL (>= 2)
Title: Assess Tumor Microsatellite Instability with a Decision Tree
Classifier from Exome Somatic Mutations
Type: Package
Author: Mini Huang
Description: A decision tree classifier for detecting microsatellite instability (MSI) in somatic mutation data from whole exome sequencing. MSI is detected based on different mutation rates in all sites as well as in simple sequence repeats. This mechanism can also be applied to sequence data of targeted gene panels with shorter sequence length.
SystemRequirements: Java
Version: 1.0.0
biocViews: Classification, SomaticMutation, Sequencing
Depends: IRanges, RWeka, rJava, R.utils, R (>= 3.2.0)
Date: 2015-06-10
NeedsCompilation: no
Packaged: 2015-06-15 12:10:59 UTC; minihuang
Repository: CRAN
Date/Publication: 2015-06-15 16:26:10

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MSIseq' ...
** package 'MSIseq' successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MSIseq'
    finding HTML links ... done
    Compute.input.variables                 html  
    MSIseq-package                          html  
    MSIseq.classify                         html  
    MSIseq.train                            html  
    NGStestdata                             html  
    NGStestseqLen                           html  
    NGStesttype                             html  
    NGStrainclass                           html  
    NGStraindata                            html  
    NGStrainseqLen                          html  
    NGStraintype                            html  
    find.mono.repeats                       html  
    read.fasta                              html  
    test.mutationNum                        html  
    train.mutationNum                       html  
** building package indices
** installing vignettes
   'MSIseq.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (MSIseq)
Making 'packages.html' ... done