[med-svn] [r-bioc-deseq2] branch upstream updated (3e47e02 -> 072b76f)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository r-bioc-deseq2.

      from  3e47e02   New upstream version 1.12.4
       new  072b76f   New upstream version 1.14.0

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                       |   10 +-
 NEWS                              |   12 +-
 R/AllClasses.R                    |    7 +-
 R/core.R                          |  102 +-
 R/expanded.R                      |    2 +-
 R/helper.R                        |   32 +-
 R/methods.R                       |    2 +-
 R/results.R                       |    7 +-
 R/rlog.R                          |    4 +-
 inst/doc/DESeq2.R                 |  239 +-
 inst/doc/DESeq2.Rnw               | 4891 ++++++++++++++++++-------------------
 inst/doc/DESeq2.pdf               |  Bin 700920 -> 673682 bytes
 man/collapseReplicates.Rd         |    3 +
 man/estimateBetaPriorVar.Rd       |    4 +-
 man/estimateDispersionsGeneEst.Rd |    7 +-
 tests/testthat/test_linear_mu.R   |   20 +
 vignettes/DESeq2.Rnw              | 4891 ++++++++++++++++++-------------------
 17 files changed, 5106 insertions(+), 5127 deletions(-)
 create mode 100644 tests/testthat/test_linear_mu.R

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