RiboProfiling

Package: RiboProfiling
Type: Package
Title: Ribosome Profiling Data Analysis: from BAM to Data
Representation and Interpretation
Version: 1.2.1
Date: 2016-02-25
Author: Alexandra Popa
Maintainer: A. Popa <alexandra.mariela.popa@gmail.com>
Description: Starting with a BAM file, this package provides the
necessary functions for quality assessment, read start position
recalibration, the counting of reads on CDS, 3'UTR, and 5'UTR,
plotting of count data: pairs, log fold-change, codon frequency
and coverage assessment, principal component analysis on codon
coverage.
biocViews: RiboSeq, Sequencing, Coverage, Alignment, QualityControl,
Software, PrincipalComponent
Depends: R (>= 3.2.2), Biostrings
Imports: BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2,
GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments,
ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf
Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene,
BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment
LazyLoad: yes
License: GPL-3
VignetteBuilder: knitr
NeedsCompilation: no
RoxygenNote: 5.0.1
Packaged: 2016-05-12 05:51:20 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'RiboProfiling' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'RiboProfiling'
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
** help
*** installing help indices
  converting help for package 'RiboProfiling'
    finding HTML links ... done
    RiboProfiling                           html  
    aroundPromoter                          html  
    codonDataCtrl                           html  
    codonIndexCovCtrl                       html  
    codonInfo                               html  
    codonPCA                                html  
    countShiftReads                         html  
    countsPlot                              html  
    ctrlGAlignments                         html  
    histMatchLength                         html  
    orfRelativePos                          html  
    plotSummarizedCov                       html  
    printPCA                                html  
    readStartCov                            html  
    readsToStartOrEnd                       html  
    riboSeqFromBAM                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'RiboProfiling'
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
* DONE (RiboProfiling)
Making 'packages.html' ... done