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 <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-deseq2.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
