Last data update: 2014.03.03

SplicingGraphs

Package: SplicingGraphs
Title: Create, manipulate, visualize splicing graphs, and assign
RNA-seq reads to them
Version: 1.12.0
Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages
License: Artistic-2.0
Description: This package allows the user to create, manipulate, and visualize
splicing graphs and their bubbles based on a gene model for a given
organism. Additionally it allows the user to assign RNA-seq reads to
the edges of a set of splicing graphs, and to summarize them in
different ways.
Maintainer: H. Pages <hpages@fredhutch.org>
Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22),
Rgraphviz (>= 2.3.7)
Imports: methods, utils, igraph, BiocGenerics, S4Vectors (>= 0.9.25),
IRanges (>= 2.3.21), GenomeInfoDb, GenomicRanges (>= 1.23.21),
GenomicFeatures, Rsamtools, GenomicAlignments, graph, Rgraphviz
Suggests: igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene,
RNAseqData.HNRNPC.bam.chr14, RUnit
Collate: utils.R igraph-utils.R SplicingGraphs-class.R
plotTranscripts-methods.R sgedgesByGene-methods.R
txpath-methods.R sgedges-methods.R sgraph-methods.R
rsgedgesByGene-methods.R bubbles-methods.R assignReads.R
countReads-methods.R toy_data.R zzz.R
biocViews: Genetics, Annotation, DataRepresentation, Visualization,
Sequencing, RNASeq, GeneExpression, AlternativeSplicing,
Transcription
NeedsCompilation: no
Packaged: 2016-05-04 04:58:04 UTC; biocbuild

● BiocViews: AlternativeSplicing, Annotation, DataRepresentation, GeneExpression, Genetics, RNASeq, Sequencing, Transcription, Visualization
● 37 images, 13 functions, 0 datasets
● Reverse Depends: 0

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'SplicingGraphs' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
** help
*** installing help indices
  converting help for package 'SplicingGraphs'
    finding HTML links ... done
    SplicingGraphs-class                    html  
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:69: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:71: missing file link 'TxDb'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:97: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:106: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:123: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:124: missing file link 'TxDb'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:126: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:130: missing file link 'TxDb'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:131: missing file link 'exonsBy'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:135: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:137: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:145: missing file link 'IntegerList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:145: missing file link 'CharacterList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:151: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:159: missing file link 'exonsBy'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:160: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:163: missing file link 'DataFrame'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:188: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:189: missing file link 'TxDb'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:220: missing file link 'exonsBy'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:222: missing file link 'TxDb'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:225: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:228: missing file link 'IntegerList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:228: missing file link 'CharacterList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/SplicingGraphs-class.Rd:231: missing file link 'DataFrame'
    SplicingGraphs-package                  html  
    TSPCsg                                  html  
    assignReads                             html  
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/assignReads.Rd:30: missing file link 'GAlignments'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/assignReads.Rd:31: missing file link 'GAlignmentPairs'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/assignReads.Rd:32: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/assignReads.Rd:51: missing file link 'readGAlignmentPairs'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/assignReads.Rd:69: missing file link 'readGAlignmentPairs'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/assignReads.Rd:74: missing file link 'scanBamFlag'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/assignReads.Rd:75: missing file link 'ScanBamParam'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/assignReads.Rd:86: missing file link 'scanBamFlag'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/assignReads.Rd:112: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/assignReads.Rd:115: missing file link 'GAlignments'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/assignReads.Rd:116: missing file link 'GAlignmentPairs'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/assignReads.Rd:118: missing file link 'readGAlignmentPairs'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/assignReads.Rd:122: missing file link 'ScanBamParam'
    bubbles-methods                         html  
    countReads-methods                      html  
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/countReads-methods.Rd:116: missing file link 'DataFrame'
    plotTranscripts-methods                 html  
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/plotTranscripts-methods.Rd:26: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/plotTranscripts-methods.Rd:28: missing file link 'TxDb'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/plotTranscripts-methods.Rd:32: missing file link 'GAlignments'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/plotTranscripts-methods.Rd:33: missing file link 'GAlignmentPairs'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/plotTranscripts-methods.Rd:66: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/plotTranscripts-methods.Rd:69: missing file link 'GAlignments'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/plotTranscripts-methods.Rd:70: missing file link 'GAlignmentPairs'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/plotTranscripts-methods.Rd:73: missing file link 'TxDb'
    rsgedgesByGene-methods                  html  
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/rsgedgesByGene-methods.Rd:81: missing file link 'GRangesList'
    sgedges-methods                         html  
    sgedgesByGene-methods                   html  
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/sgedgesByGene-methods.Rd:21: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/sgedgesByGene-methods.Rd:27: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/sgedgesByGene-methods.Rd:63: missing file link 'GRangesList'
    sgraph-methods                          html  
    toy_data                                html  
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/toy_data.Rd:36: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/toy_data.Rd:39: missing file link 'GAlignments'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/toy_data.Rd:40: missing file link 'GAlignmentPairs'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/toy_data.Rd:44: missing file link 'TxDb'
    txpath-methods                          html  
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/txpath-methods.Rd:35: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/txpath-methods.Rd:69: missing file link 'GRangesList'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/txpath-methods.Rd:72: missing file link 'GAlignments'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/txpath-methods.Rd:73: missing file link 'GAlignmentPairs'
Rd warning: /tmp/Rtmp0kSE7E/R.INSTALL7384796b6aff/SplicingGraphs/man/txpath-methods.Rd:82: missing file link 'ScanBamParam'
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::from' by 'Rgraphviz::from' when loading 'SplicingGraphs'
Warning: replacing previous import 'IRanges::to' by 'Rgraphviz::to' when loading 'SplicingGraphs'
* DONE (SplicingGraphs)
Making 'packages.html' ... done

Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO