[med-svn] [r-bioc-cummerbund] branch master updated (fc6ac98 -> 5b42143)

[Andreas Tille]

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

      from  fc6ac98   Upload to unstable
       new  185e6e7   Imported Upstream version 2.8.0
       new  7adf88b   Merge tag 'upstream/2.8.0'
       new  63317a9   New upstream version
       new  a57d710   cme fix dpkg-control
       new  dd39e3e   Update dependencies
       new  5b42143   Update copyright info

The 6 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
 debian/changelog                         |   9 +
 debian/control                           |  13 +-
 debian/copyright                         |  21 +-
 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 +++++-
 43 files changed, 1415 insertions(+), 243 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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