caRpools

Package: caRpools
Type: Package
Title: CRISPR AnalyzeR for Pooled CRISPR Screens
Version: 0.83
Date: 2015-12-06
Author: Jan Winter, Florian Heigwer
Maintainer: Jan Winter <jan.winter@dkfz-heidelberg.de>
Description: CRISPR-Analyzer for pooled CRISPR screens (caRpools) provides an end-to-end analysis of CRISPR screens including quality control, hit candidate analysis, visualization and automated report generation using R markdown. Needs MAGeCK (http://sourceforge.net/p/mageck/wiki/Home/), bowtie2 for all functions. CRISPR (clustered regularly interspaced short palindromic repeats) is a method to perform genome editing. See <https://en.wikipedia.org/wiki/CRISPR> for more information on
CRISPR.
Depends: R (>= 3.1.0)
Imports:
rmarkdown,VennDiagram,DESeq2,sm,biomaRt,seqinr,scatterplot3d,xlsx
Suggests: BiocGenerics, knitr, stringi
SystemRequirements: MAGeCK (=0.51, from
http://sourceforge.net/p/mageck/wiki/Home/), bowtie2
(http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
License: GPL
URL: http://www.crispr-analyzer.de
https://github.com/boutroslab/caRpools
BugReports: https://github.com/boutroslab/caRpools
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2015-12-05 18:38:31 UTC; janwinter
Repository: CRAN
Date/Publication: 2015-12-06 13:31:59

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'caRpools' ...
** package 'caRpools' successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'caRpools'
    finding HTML links ... done
    CONTROL1                                html  
    CONTROL1.g                              html  
    CONTROL2                                html  
    CONTROL2.g                              html  
    TREAT1                                  html  
    TREAT1.g                                html  
    TREAT2                                  html  
    TREAT2.g                                html  
    aggregatetogenes                        html  
    caRpools                                html  
    carpools.hit.overview                   html  
    carpools.hit.scatter                    html  
    carpools.hit.sgrna                      html  
    carpools.hitident                       html  
    carpools.raw.genes                      html  
    carpools.read.count.vs                  html  
    carpools.read.depth                     html  
    carpools.read.distribution              html  
    carpools.reads.genedesigns              html  
    carpools.sgrna.table                    html  
    carpools.waterfall.pval                 html  
    check.caRpools                          html  
    compare.analysis                        html  
    d.CONTROL1                              html  
    d.CONTROL2                              html  
    d.TREAT1                                html  
    d.TREAT2                                html  
    data.extract                            html  
    final.table                             html  
    gene.remove                             html  
    generate.hits                           html  
    get.gene.info                           html  
    libFILE                                 html  
    load.file                               html  
    load.packages                           html  
    referencefile                           html  
    stat.DESeq                              html  
    stat.mageck                             html  
    stat.wilcox                             html  
    stats.data                              html  
    unmapped.genes                          html  
    use.caRpools                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (caRpools)
Making 'packages.html' ... done