bakR: Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets
Several implementations of a novel Bayesian hierarchical statistical model of nucleotiderecoding 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 kineticsof RNA metabolism (e.g., RNA degradation rate constants), which is notably lackingin standard RNA-seq data. The statistical model makes maximal use of these high-throughputdatasets by sharing information across transcripts to significantly improveuncertainty quantification and increase statistical power. 'bakR' includes a maximallyefficient 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-testadjusted statistical inference with the output of these model implementations tohelp biologists separate signal from background. Methods to automatically visualize keyresults and detect batch effects are also provided.
| Version: | 1.0.1 |
| Depends: | R (≥ 3.5.0) |
| Imports: | purrr, methods,Rcpp (≥ 0.12.0),RcppParallel (≥ 5.0.1),rstan (≥ 2.26.0),rstantools (≥ 2.1.1),dplyr,tidyr, stats,magrittr,Hmisc,ggplot2,data.table |
| LinkingTo: | BH (≥ 1.66.0),Rcpp (≥ 0.12.0),RcppEigen (≥ 0.3.3.3.0),RcppParallel (≥ 5.0.1),rstan (≥ 2.26.0),StanHeaders (≥2.26.0) |
| Suggests: | rmarkdown,knitr,DESeq2,pheatmap,Ckmeans.1d.dp,corrplot |
| Published: | 2024-01-13 |
| DOI: | 10.32614/CRAN.package.bakR |
| Author: | Isaac Vock [aut, cre] |
| Maintainer: | Isaac Vock <isaac.vock at gmail.com> |
| BugReports: | https://github.com/simonlabcode/bakR/issues/ |
| License: | MIT + fileLICENSE |
| URL: | https://simonlabcode.github.io/bakR/ |
| NeedsCompilation: | yes |
| SystemRequirements: | GNU make C++17 |
| Materials: | README,NEWS |
| CRAN checks: | bakR results |
Documentation:
| Reference manual: | bakR.html ,bakR.pdf |
| Vignettes: | Differential-Synth (source,R code) Dropout (source,R code) Getting-Started (source,R code) NSS (source,R code) Troubleshooting (source,R code) bakR-Fn (source,R code) bakR-Quickstart (source,R code) |
Downloads:
| Package source: | bakR_1.0.1.tar.gz |
| Windows binaries: | r-devel:bakR_1.0.1.zip, r-release:bakR_1.0.1.zip, r-oldrel:bakR_1.0.1.zip |
| macOS binaries: | r-release (arm64):bakR_1.0.1.tgz, r-oldrel (arm64):bakR_1.0.1.tgz, r-release (x86_64):bakR_1.0.1.tgz, r-oldrel (x86_64):bakR_1.0.1.tgz |
| Old sources: | bakR archive |
Linking:
Please use the canonical formhttps://CRAN.R-project.org/package=bakRto link to this page.