denoiSeq
Differential Expression Analysis Using a Bottom-Up Model
Description
Given count data from two conditions, it determines which transcripts are differentially expressed across the two conditions using Bayesian inference of the parameters of a bottom-up model for PCR amplification. This model is developed in Ndifon Wilfred, Hilah Gal, Eric Shifrut, Rina Aharoni, Nissan Yissachar, Nir Waysbort, Shlomit Reich Zeliger, Ruth Arnon, and Nir Friedman (2012), <http://www.pnas.org/content/109/39/15865.full>, and results in a distribution for the counts that is a superposition of the binomial and negative binomial distribution.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | ERROR |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (1 non-OK)
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building 'denoiSeq-vignette.Rmd' using rmarkdown ! Package pdftex.def Error: File `555cc84ed893abb1597114c5ef12f98b6f5831cd.pdf' not found: using draft setting. Error: processing vignette 'denoiSeq-vignette.Rmd' failed with diagnostics: LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/denoiSeq.Rcheck/vign_test/denoiSeq/vignettes/denoiSeq-vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See denoiSeq-vignette.log for more info. --- failed re-building 'denoiSeq-vignette.Rmd' SUMMARY: processing the following file failed: 'denoiSeq-vignette.Rmd' Error: Vignette re-building failed. Execution halted
Check History
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 30, 2026
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building 'denoiSeq-vignette.Rmd' using rmarkdown ! Package pdftex.def Error: File `555cc84ed893abb1597114c5ef12f98b6f5831cd.pdf' not found: using draft setting. Error: processing vignette 'denoiSeq-vignette ...[truncated]... x/r/#debugging for debugging tips. See denoiSeq-vignette.log for more info. --- failed re-building 'denoiSeq-vignette.Rmd' SUMMARY: processing the following file failed: 'denoiSeq-vignette.Rmd' Error: Vignette re-building failed. Execution halted