Other packages > Find by keyword >

bakR  

Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets
View on CRAN: Click here


Download and install bakR package within the R console
Install from CRAN:
install.packages("bakR")

Install from Github:
library("remotes")
install_github("cran/bakR")

Install by package version:
library("remotes")
install_version("bakR", "1.0.1")



Attach the package and use:
library("bakR")
Maintained by
Isaac Vock
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-10-10
Latest Update: 2024-01-13
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) ). 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.
How to cite:
Isaac Vock (2022). bakR: Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets. R package version 1.0.1, https://cran.r-project.org/web/packages/bakR. Accessed 26 Aug. 2026.
Previous versions and publish date:
(2026-07-09 07:20), 0.2.4 (2022-10-10 18:10), 0.4.0 (2023-03-14 17:10), 1.0.0 (2023-06-29 23:20)
Other packages that cited bakR R package
View bakR citation profile
Other R packages that bakR depends, imports, suggests or enhances
Complete documentation for bakR
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
SelvarMix  
Regularization for Variable Selection in Model-Based Clustering and Discriminant Analysis
Performs a regularization approach to variable selection in themodel-based clustering and classifica ...
Download / Learn more Package Citations See dependency  
clinUtils  
General Utility Functions for Analysis of Clinical Data
Utility functions to facilitate the import, the reporting and analysis of clinical data. Example ...
Download / Learn more Package Citations See dependency  
ncodeR  
Techniques for Automated Classifiers
A set of techniques that can be used to develop, validate, and implement automated classifiers. A po ...
Download / Learn more Package Citations See dependency  
leafgl  
High-Performance 'WebGl' Rendering for Package 'leaflet'
Provides bindings to the 'Leaflet.glify' JavaScript library which extends the 'leaflet' JavaScript l ...
Download / Learn more Package Citations See dependency  
RCytoGPS  
Using Cytogenetics Data in R
Defines classes and methods to process text-based cytogenetics using the CytoGPS web site, then imp ...
Download / Learn more Package Citations See dependency  

28,332

R Packages

239,283

Dependencies

75,113

Author Associations

28,333

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA