[med-svn] [r-bioc-deseq2] branch upstream updated (a9c33f5 -> e4d563b)
Andreas Tille
tille at debian.org
Mon Oct 2 20:31:23 UTC 2017
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 a9c33f5 New upstream version 1.14.1
new e4d563b New upstream version 1.16.1
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 | 11 +-
NAMESPACE | 2 +
NEWS | 71 +-
R/RcppExports.R | 14 +-
R/core.R | 863 +++-------
R/fitNbinomGLMs.R | 375 +++++
R/helper.R | 178 ++-
R/methods.R | 38 +-
R/plots.R | 63 +-
R/results.R | 72 +-
R/wrappers.R | 108 ++
build/vignette.rds | Bin 231 -> 219 bytes
inst/CITATION | 8 +-
inst/doc/DESeq2.R | 389 +++--
inst/doc/DESeq2.Rmd | 2420 +++++++++++++++++++++++++++++
inst/doc/DESeq2.Rnw | 2414 ----------------------------
inst/doc/DESeq2.html | 1756 +++++++++++++++++++++
inst/doc/DESeq2.pdf | Bin 672224 -> 0 bytes
man/DESeq.Rd | 16 +-
man/DESeq2-package.Rd | 7 +-
man/DESeqDataSet.Rd | 4 +-
man/DESeqResults.Rd | 2 +-
man/DESeqTransform.Rd | 2 +-
man/coef.Rd | 1 -
man/collapseReplicates.Rd | 1 -
man/counts.Rd | 8 +-
man/design.Rd | 2 +-
man/dispersionFunction.Rd | 5 +-
man/dispersions.Rd | 11 +-
man/estimateBetaPriorVar.Rd | 2 +-
man/estimateDispersions.Rd | 1 -
man/estimateDispersionsGeneEst.Rd | 6 +-
man/estimateSizeFactors.Rd | 27 +-
man/estimateSizeFactorsForMatrix.Rd | 7 +-
man/fpkm.Rd | 1 -
man/fpm.Rd | 1 -
man/lfcShrink.Rd | 43 +
man/makeExampleDESeqDataSet.Rd | 1 -
man/nbinomLRT.Rd | 17 +-
man/nbinomWaldTest.Rd | 53 +-
man/normTransform.Rd | 1 -
man/normalizationFactors.Rd | 5 +-
man/normalizeGeneLength.Rd | 1 -
man/plotCounts.Rd | 15 +-
man/plotDispEsts.Rd | 13 +-
man/plotMA.Rd | 10 +-
man/plotPCA.Rd | 1 -
man/plotSparsity.Rd | 1 -
man/replaceOutliers.Rd | 2 +-
man/results.Rd | 14 +-
man/rlog.Rd | 2 +-
man/show.Rd | 1 -
man/sizeFactors.Rd | 8 +-
man/summary.Rd | 6 +-
man/unmix.Rd | 43 +
man/varianceStabilizingTransformation.Rd | 10 +-
man/vst.Rd | 1 -
src/DESeq2.cpp | 103 +-
src/RcppExports.cpp | 48 +-
tests/testthat/test_1vs1.R | 9 +-
tests/testthat/test_DESeq.R | 37 +-
tests/testthat/test_LRT.R | 20 +-
tests/testthat/test_LRT_prior.R | 13 -
tests/testthat/test_QR.R | 18 +-
tests/testthat/test_addMLE.R | 32 +-
tests/testthat/test_betaFitting.R | 81 +-
tests/testthat/test_collapse.R | 15 +-
tests/testthat/test_construction_errors.R | 69 +-
tests/testthat/test_counts_input.R | 27 +-
tests/testthat/test_custom_filt.R | 47 +-
tests/testthat/test_disp_fit.R | 211 ++-
tests/testthat/test_dispersions.R | 51 +-
tests/testthat/test_edge_case.R | 95 +-
tests/testthat/test_factors.R | 19 +-
tests/testthat/test_fpkm.R | 13 +-
tests/testthat/test_frozen_transform.R | 49 +-
tests/testthat/test_htseq.R | 17 +-
tests/testthat/test_interactions.R | 18 +-
tests/testthat/test_lfcShrink.R | 16 +
tests/testthat/test_linear_mu.R | 43 +-
tests/testthat/test_methods.R | 19 +-
tests/testthat/test_model_matrix.R | 53 +-
tests/testthat/test_nbinomWald.R | 45 +-
tests/testthat/test_optim.R | 76 +-
tests/testthat/test_outlier.R | 132 +-
tests/testthat/test_parallel.R | 113 +-
tests/testthat/test_plots.R | 53 +-
tests/testthat/test_results.R | 310 ++--
tests/testthat/test_rlog.R | 45 +-
tests/testthat/test_size_factor.R | 66 +-
tests/testthat/test_tximport.R | 44 +-
tests/testthat/test_unmix_samples.R | 51 +
tests/testthat/test_vst.R | 57 +-
tests/testthat/test_weights.R | 91 ++
tests/testthat/test_zero_zero.R | 18 -
vignettes/DESeq2.Rmd | 2420 +++++++++++++++++++++++++++++
vignettes/DESeq2.Rnw | 2414 ----------------------------
vignettes/library.bib | 22 +-
vignettes/sed_call | 1 +
99 files changed, 9278 insertions(+), 6937 deletions(-)
create mode 100644 R/fitNbinomGLMs.R
create mode 100644 R/wrappers.R
create mode 100644 inst/doc/DESeq2.Rmd
delete mode 100644 inst/doc/DESeq2.Rnw
create mode 100644 inst/doc/DESeq2.html
delete mode 100644 inst/doc/DESeq2.pdf
create mode 100644 man/lfcShrink.Rd
create mode 100644 man/unmix.Rd
delete mode 100644 tests/testthat/test_LRT_prior.R
create mode 100644 tests/testthat/test_lfcShrink.R
create mode 100644 tests/testthat/test_unmix_samples.R
create mode 100644 tests/testthat/test_weights.R
delete mode 100644 tests/testthat/test_zero_zero.R
create mode 100644 vignettes/DESeq2.Rmd
delete mode 100644 vignettes/DESeq2.Rnw
create mode 100644 vignettes/sed_call
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