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 13 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 | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| 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 (2 non-OK)
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.
Check History
NOTE 11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
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.
ERROR 10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026
package dependencies
Package required but not available: ‘Hmisc’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
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.
NOTE 11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 10, 2026
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.
ERROR 10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE May 3, 2026
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.
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> ...[truncated]... -Fn.Rmd’ --- re-building ‘bakR-Quickstart.Rmd’ using rmarkdown --- finished re-building ‘bakR-Quickstart.Rmd’ SUMMARY: processing the following files failed: ‘Differential-Synth.Rmd’ ‘NSS.Rmd’ Error: Vignette re-building failed. Execution halted
NOTE 9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 2026
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
ERROR 8 OK · 5 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 2026
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.
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.6/bakR.Rcheck/00install.out' for details.
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
NOTE 9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 3, 2026
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
ERROR 9 OK · 4 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 3, 2026
dependencies in R code
Namespaces in Imports field not imported from: ‘RcppParallel’ ‘rstantools’ All declared Imports should be used.
whether package can be installed
Installation failed. See ‘/data/gannet/ripley/R/packages/tests-devel/bakR.Rcheck/00install.out’ for details.
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
NOTE 9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
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