Analyze and Integrate Any Type of Nucleotide Recoding RNA-Seq Data
Average parameter estimates across replicates, and regularize variance...
Get contrasts of estimated parameters
Correct for experimental/bioinformatic dropout of labeled RNA.
Generate a fraction_design table for EstimateFractions.
Deconvolve multi-feature fractions.
Estimate fractions of each RNA population.
Estimate isoform-specific fraction news (or more generally "fractions"...
Estimate kinetic parameters
Estimate mutation rates
EZbakRArrowData object helper function for users
EZbakRData object helper function for users
EZbakRFractions helper function for users
EZbakRKinetics helper function for users
Generalized dynamical systems modeling
Easily get EZbakR table of estimates of interest
Make an MAPlot from EZbakR comparison
Make an MAPlot from EZbakR comparison
Run quality control checks
Run quality control checks
Run quality control checks
Run quality control checks
Simulate NR-seq data for multiple replicates of multiple biological co...
Make a VolcanoPlot from EZbakR comparison
Get normalized read counts from either a cB table or EZbakRFractions...
Import transcript isoform quantification into EZbakRData object
EZbakRArrowData object constructor for internal use
EZbakRDataobject constructor for internal use
EZbakRFractions object constructor
EZbakRKinetics object constructor
Normalize for experimental/bioinformatic dropout of labeled RNA.
Print method for EZbakRArrowData objects
Print method for EZbakRData objects
Simple simulation function
Simulation of generalized dynamical system model.
Simulation of transcript isoform kinetic parameters.
Simulate NR-seq data for multiple replicates of multiple biological co...
Simulate one replicate of multi-label NR-seq data
Simulate a single replicate of NR-seq data
EZbakRArrowData EZbakRArrowData validator
EZbakRDataobject validator
EZbakRFractions object validator
EZbakRKinetics object validator
Vectorized simulation of one replicate of multi-label NR-seq data
Make plots to visually assess dropout trends
A complete rewrite and reimagining of 'bakR' (see 'Vock et al.' (2025) <doi:10.1371/journal.pcbi.1013179>). Designed to support a wide array of analyses of nucleotide recoding RNA-seq (NR-seq) datasets of any type, including TimeLapse-seq/SLAM-seq/TUC-seq, Start-TimeLapse-seq (STL-seq), TT-TimeLapse-seq (TT-TL-seq), and subcellular NR-seq. 'EZbakR' extends standard NR-seq standard NR-seq mutational modeling to support multi-label analyses (e.g., 4sU and 6sG dual labeling), and implements an improved hierarchical model to better account for transcript-to-transcript variance in metabolic label incorporation. 'EZbakR' also generalized dynamical systems modeling of NR-seq data to support analyses of premature mRNA processing and flow between subcellular compartments. Finally, 'EZbakR' implements flexible and well-powered comparative analyses of all estimated parameters via design matrix-specified generalized linear modeling.
Useful links