[med-svn] [r-bioc-deseq2] branch upstream updated (e4d563b -> 36eda24)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

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

      from  e4d563b   New upstream version 1.16.1
       new  36eda24   New upstream version 1.18.0

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                               |   9 +-
 NAMESPACE                                 |   4 +
 NEWS                                      |  18 +
 R/AllClasses.R                            |  41 +-
 R/AllGenerics.R                           |   8 +
 R/RcppExports.R                           |   6 +-
 R/core.R                                  |  29 +-
 R/helper.R                                |  76 +--
 R/lfcShrink.R                             | 318 ++++++++++++
 R/methods.R                               |  32 +-
 R/plots.R                                 |  43 +-
 R/results.R                               |  12 +-
 build/vignette.rds                        | Bin 219 -> 221 bytes
 inst/doc/DESeq2.R                         | 101 ++--
 inst/doc/DESeq2.Rmd                       | 444 ++++++++++-------
 inst/doc/DESeq2.html                      | 802 ++++++++++++++++++------------
 man/DESeq.Rd                              |   6 +-
 man/DESeq2-package.Rd                     |   4 +-
 man/DESeqResults.Rd                       |   4 +-
 man/estimateDispersionsGeneEst.Rd         |   4 +-
 man/lfcShrink.Rd                          | 102 +++-
 man/normTransform.Rd                      |   2 +-
 man/priorInfo.Rd                          |  30 ++
 src/RcppExports.cpp                       |  18 +-
 tests/testthat/test_construction_errors.R |   2 +
 tests/testthat/test_interactions.R        |  10 +-
 tests/testthat/test_lfcShrink.R           |  56 ++-
 tests/testthat/test_nbinomWald.R          |  10 +
 tests/testthat/test_parallel.R            |  14 +
 tests/testthat/test_results.R             |  15 +-
 vignettes/DESeq2.Rmd                      | 444 ++++++++++-------
 vignettes/library.bib                     |  69 ++-
 32 files changed, 1825 insertions(+), 908 deletions(-)
 create mode 100644 R/lfcShrink.R
 create mode 100644 man/priorInfo.Rd

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