[med-svn] [r-bioc-cummerbund] 02/06: Merge tag 'upstream/2.8.0'

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-bioc-cummerbund.

commit 7adf88b80adf32cec7c5664e645fb35dfa1a359b
Merge: fc6ac98 185e6e7
Author: Andreas Tille <tille at debian.org>
Date:   Wed Oct 22 13:24:29 2014 +0200

    Merge tag 'upstream/2.8.0'
    
    Upstream version 2.8.0

 DESCRIPTION                              |  23 +--
 NAMESPACE                                |   8 +-
 R/AllClasses.R                           |   3 +-
 R/AllGenerics.R                          |   9 +-
 R/database-setup.R                       | 128 +++++++++++-
 R/methods-CuffData.R                     | 291 ++++++++++++++++++++++-----
 R/methods-CuffFeature.R                  |  48 ++++-
 R/methods-CuffFeatureSet.R               | 332 ++++++++++++++++++++++++++++---
 R/methods-CuffGene.R                     |  85 +++++++-
 R/methods-CuffSet.R                      |  59 ++++--
 R/tools.R                                |  77 +++++--
 build/vignette.rds                       | Bin 302 -> 303 bytes
 data/sampleData.rda                      | Bin 0 -> 158 bytes
 inst/NEWS                                |  31 +++
 inst/doc/cummeRbund-example-workflow.pdf | Bin 198250 -> 198287 bytes
 inst/doc/cummeRbund-manual.R             | 130 +++++++-----
 inst/doc/cummeRbund-manual.Rnw           |  59 +++++-
 inst/doc/cummeRbund-manual.pdf           | Bin 1546156 -> 1563970 bytes
 inst/reports/styles/report_style.css     | 124 ++++++++++++
 man/CuffData-class.Rd                    |   2 -
 man/CuffFeature-class.Rd                 |   1 +
 man/CuffGene-class.Rd                    |   3 +
 man/CuffSet-class.Rd                     |   7 +-
 man/JSdist.Rd                            |   5 +-
 man/QCplots.Rd                           |   5 +-
 man/csCluster.Rd                         |   5 +-
 man/csClusterPlot.Rd                     |   5 +-
 man/csHeatmap.Rd                         |  13 ++
 man/csScatter.Rd                         |   2 +-
 man/diffData.Rd                          |   7 +
 man/dimensionality.Rd                    |   7 +-
 man/dispersionPlot.Rd                    |   2 +
 man/exploratory.Rd                       |  63 ++++++
 man/expressionPlot.Rd                    |   5 +-
 man/featureNames.Rd                      |   1 -
 man/fpkmMatrix.Rd                        |   1 +
 man/getSig.Rd                            |   8 +-
 man/readCufflinks.Rd                     |   6 +-
 man/replicates.Rd                        |   1 +
 vignettes/cummeRbund-manual.Rnw          |  59 +++++-
 40 files changed, 1390 insertions(+), 225 deletions(-)

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