soGGi

Package: soGGi
Type: Package
Title: Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate
plots Summarised Over Grouped Genomic Intervals
Version: 1.4.4
Date: 2015-12-02
Author: Gopuraja Dharmalingam, Tom Carroll
Maintainer: Tom Carroll <tc.infomatics@gmail.com>
Description: The soGGi package provides a toolset to create genomic
interval aggregate/summary plots of signal or motif occurence
from BAM and bigWig files as well as PWM, rlelist, GRanges and
GAlignments Bioconductor objects. soGGi allows for
normalisation, transformation and arithmetic operation on and
between summary plot objects as well as grouping and subsetting
of plots by GRanges objects and user supplied metadata. Plots
are created using the GGplot2 libary to allow user defined
manipulation of the returned plot object. Coupled together,
soGGi features a broad set of methods to visualise genomics
data in the context of groups of genomic intervals such as
genes, superenhancers and transcription factor binding events.
biocViews: Sequencing, ChIPSeq, Coverage
License: GPL (>= 3)
LazyLoad: yes
Depends: R (>= 3.2.0), BiocGenerics, SummarizedExperiment
Imports: methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb,
GenomicRanges, Biostrings, Rsamtools, GenomicAlignments,
rtracklayer, preprocessCore, chipseq, BiocParallel
Collate: 'allClasses.r' 'motifTools.R' 'peakTransforms.r' 'plots.R'
'soggi.R'
VignetteBuilder: knitr
Suggests: testthat, BiocStyle, knitr
NeedsCompilation: no
Packaged: 2016-05-16 05:25:43 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'soGGi' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi'
** help
*** installing help indices
  converting help for package 'soGGi'
    finding HTML links ... done
    ChIPprofile                             html  
    Ops                                     html  
    chipExampleBig                          html  
    findconsensusRegions                    html  
    groupByOverlaps                         html  
    ik_Example                              html  
    ik_Profiles                             html  
    manipulateObjects                       html  
    normalise                               html  
    normaliseQuantiles                      html  
    orientBy                                html  
    plotRegion                              html  
    pwmCov                                  html  
    pwmToCoverage                           html  
    singleGRange                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi'
* DONE (soGGi)
Making 'packages.html' ... done