[med-svn] [r-bioc-deseq2] branch master updated (39b9844 -> a04112d)

[Andreas Tille]

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

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

      from  39b9844   upload to unstable
       new  d4b3556   Secure URI in watch file
       new  0aa0e5c   New upstream version
       new  36eda24   New upstream version 1.18.0
       new  10f4722   Update upstream source from tag 'upstream/1.18.0'
       new  00859d1   Refresh patches
       new  a04112d   Upload to unstable

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                               |   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
 debian/changelog                          |   7 +
 debian/patches/remove-locfit              |  24 +-
 debian/watch                              |   2 +-
 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 ++-
 35 files changed, 1845 insertions(+), 921 deletions(-)
 create mode 100644 R/lfcShrink.R
 create mode 100644 man/priorInfo.Rd

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