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cff-version: 1.2.0
message: 'To cite package "bakR" in publications use:'
type: software
license: MIT
title: 'bakR: Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets'
version: 1.0.1
doi: 10.32614/CRAN.package.bakR
abstract: 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) <https://doi.org/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.
authors:
- family-names: Vock
  given-names: Isaac
  email: isaac.vock@gmail.com
  orcid: https://orcid.org/0000-0002-7178-6886
repository: https://cran.r-universe.dev
repository-code: https://github.com/simonlabcode/bakR/issues/
commit: 60faee4f4a732547f0f21f23dbee4514cef09bf6
url: https://simonlabcode.github.io/bakR/
date-released: '2024-01-14'
contact:
- family-names: Vock
  given-names: Isaac
  email: isaac.vock@gmail.com
  orcid: https://orcid.org/0000-0002-7178-6886