[med-svn] [r-bioc-deseq2] 02/06: Updated version 1.16.1 from 'upstream/1.16.1'
Andreas Tille
tille at debian.org
Mon Oct 2 20:31:22 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-deseq2.
commit a929bbd60b961eb507a47ab51c6f1653564c4520
Merge: 66b74b0 e4d563b
Author: Andreas Tille <tille at debian.org>
Date: Mon Oct 2 22:00:40 2017 +0200
Updated version 1.16.1 from 'upstream/1.16.1'
with Debian dir 2fabd42ca0e4c8351489afdcec528c2ffe4e590b
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(-)
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