[med-svn] [r-bioc-cummerbund] branch upstream updated (d39d6a1 -> 185e6e7)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository r-bioc-cummerbund.

      from  d39d6a1   Imported Upstream version 2.6.1
       new  185e6e7   Imported Upstream version 2.8.0

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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(-)
 create mode 100644 data/sampleData.rda
 create mode 100644 inst/reports/styles/report_style.css
 create mode 100644 man/exploratory.Rd

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