bakR
Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets
Description
Several implementations of a novel Bayesian hierarchical statistical model of nucleotide recoding RNA-seq experiments (NR-seq; TimeLapse-seq, SLAM-seq, TUC-seq, etc.) for analyzing and comparing NR-seq datasets (see 'Vock and Simon' (2023) <doi:10.1261/rna.079451.122>). NR-seq is a powerful extension of RNA-seq that provides information about the kinetics of RNA metabolism (e.g., RNA degradation rate constants), which is notably lacking in standard RNA-seq data. The statistical model makes maximal use of these high-throughput datasets by sharing information across transcripts to significantly improve uncertainty quantification and increase statistical power. 'bakR' includes a maximally efficient implementation of this model for conservative initial investigations of datasets. 'bakR' also provides more highly powered implementations using the probabilistic programming language 'Stan' to sample from the full posterior distribution. 'bakR' performs multiple-test adjusted statistical inference with the output of these model implementations to help biologists separate signal from background. Methods to automatically visualize key results and detect batch effects are also provided.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | ERROR |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| 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 (16 non-OK)
re-building of vignette outputs
Error(s) in re-building vignettes:
...
--- re-building ‘Differential-Synth.Rmd’ using rmarkdown
Quitting from Differential-Synth.Rmd:28-42 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'DESeq2'
---
Backtrace:
▆
1. └─base::library(DESeq2)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Differential-Synth.Rmd' failed with diagnostics:
there is no package called 'DESeq2'
--- failed re-building ‘Differential-Synth.Rmd’
--- re-building ‘Dropout.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Dropout.Rmd’
--- re-building ‘Getting-Started.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Getting-Started.Rmd’
--- re-building ‘NSS.Rmd’ using rmarkdown
Quitting from NSS.Rmd:31-46 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'DESeq2'
---
Backtrace:
▆
1. └─base::library(DESeq2)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'NSS.Rmd' failed with diagnostics:
there is no package called 'DESeq2'
--- failed re-building ‘NSS.Rmd’
--- re-building ‘Troubleshooting.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Troubleshooting.Rmd’
--- re-building ‘bakR-Fn.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘bakR-Fn.Rmd’
--- re-building ‘bakR-Quickstart.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘bakR-Quickstart.Rmd’
SUMMARY: processing the following files failed:
‘Differential-Synth.Rmd’ ‘NSS.Rmd’
Error: Vignette re-building failed.
Execution halted
*
dependencies in R code
Namespaces in Imports field not imported from: ‘RcppParallel’ ‘rstantools’ All declared Imports should be used.
dependencies in R code
Namespaces in Imports field not imported from: ‘RcppParallel’ ‘rstantools’ All declared Imports should be used.
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for GNU extensions in Makefiles
GNU make is a SystemRequirements.
installed package size
installed size is 103.3Mb
sub-directories of 1Mb or more:
libs 101.5Mb
for GNU extensions in Makefiles
GNU make is a SystemRequirements.
installed package size
installed size is 105.5Mb
sub-directories of 1Mb or more:
libs 103.7Mb
installed package size
installed size is 7.1Mb
sub-directories of 1Mb or more:
libs 5.4Mb
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Check History
ERROR 8 OK · 5 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 9, 2026
re-building of vignette outputs
Error(s) in re-building vignettes:
...
--- re-building ‘Differential-Synth.Rmd’ using rmarkdown
Quitting from Differential-Synth.Rmd:28-42 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'DESeq2'
---
Backtrace:
▆
1. └─base::library(DESeq2)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Differential-Synth.Rmd' failed
dependencies in R code
Namespaces in Imports field not imported from: ‘RcppParallel’ ‘rstantools’ All declared Imports should be used.
dependencies in R code
Namespaces in Imports field not imported from: ‘RcppParallel’ ‘rstantools’ All declared Imports should be used.
installed package size
installed size is 103.3Mb
sub-directories of 1Mb or more:
libs 101.5Mb
installed package size
installed size is 105.5Mb
sub-directories of 1Mb or more:
libs 103.7Mb
installed package size
installed size is 7.1Mb
sub-directories of 1Mb or more:
libs 5.4Mb