R: Analyze and Integrate Any Type of Nucleotide Recoding RNA-Seq Data

# Analyze and Integrate Any Type of Nucleotide Recoding RNA-Seq Data

## Documentation for package ‘EZbakR’ version 0.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

AverageAndRegularize | Average parameter estimates across replicates, and regularize variance estimates
CompareParameters | Get contrasts of estimated parameters
CorrectDropout | Correct for experimental/bioinformatic dropout of labeled RNA.
create_fraction_design | Generate a 'fraction_design' table for 'EstimateFractions'.
DeconvolveFractions | Deconvolve multi-feature fractions.
EstimateFractions | Estimate fractions of each RNA population.
EstimateFractions.EZbakRArrowData | Estimate fractions of each RNA population.
EstimateFractions.EZbakRData | Estimate fractions of each RNA population.
EstimateIsoformFractions | Estimate isoform-specific fraction news (or more generally "fractions").
EstimateKinetics | Estimate kinetic parameters
EstimateMutRates | Estimate mutation rates
EstimateMutRates.EZbakRArrowData | Estimate mutation rates
EstimateMutRates.EZbakRData | Estimate mutation rates
example_cB | Example cB table
example_metadf | Example metadf
EZbakRArrowData | 'EZbakRArrowData' object helper function for users
EZbakRData | 'EZbakRData' object helper function for users
EZbakRFractions | 'EZbakRFractions' helper function for users
EZbakRKinetics | 'EZbakRKinetics' helper function for users
EZDynamics | Generalized dynamical systems modeling
EZget | Easily get EZbakR table of estimates of interest
EZMAPlot | Make an MAPlot from EZbakR comparison
EZpcaPlot | Make an MAPlot from EZbakR comparison
EZQC | Run quality control checks
EZQC.EZbakRArrowData | Run quality control checks
EZQC.EZbakRData | Run quality control checks
EZQC.EZbakRFractions | Run quality control checks
EZSimulate | Simulate NR-seq data for multiple replicates of multiple biological conditions
EZVolcanoPlot | Make a VolcanoPlot from EZbakR comparison
get_normalized_read_counts | Get normalized read counts from either a cB table or 'EZbakRFractions' object.
get_normalized_read_counts.EZbakRData | Get normalized read counts from either a cB table or 'EZbakRFractions' object.
get_normalized_read_counts.EZbakRFractions | Get normalized read counts from either a cB table or 'EZbakRFractions' object.
ImportIsoformQuant | Import transcript isoform quantification into EZbakRData object
new_EZbakRArrowData | 'EZbakRArrowData' object constructor for internal use
new_EZbakRData | 'EZbakRDataobject' constructor for internal use
new_EZbakRFractions | 'EZbakRFractions' object constructor
new_EZbakRKinetics | 'EZbakRKinetics' object constructor
NormalizeForDropout | Normalize for experimental/bioinformatic dropout of labeled RNA.
ode_models | Example ODE model graphs and formulas
print.EZbakRArrowData | Print method for 'EZbakRArrowData' objects
print.EZbakRData | Print method for 'EZbakRData' objects
SimpleSim | Simple simulation function
SimulateDynamics | Simulation of generalized dynamical system model.
SimulateIsoforms | Simulation of transcript isoform kinetic parameters.
SimulateMultiCondition | Simulate NR-seq data for multiple replicates of multiple biological conditions
SimulateMultiLabel | Simulate one replicate of multi-label NR-seq data
SimulateOneRep | Simulate a single replicate of NR-seq data
standard_fraction_design | Standard 'fraction_design' table for 'EstimateFractions'
tilac_fraction_design | TILAC 'fraction_design' table for 'EstimateFractions'
validate_EZbakRArrowData | 'EZbakRArrowData' EZbakRArrowData validator
validate_EZbakRData | 'EZbakRDataobject' validator
validate_EZbakRFractions | 'EZbakRFractions' object validator
validate_EZbakRKinetics | 'EZbakRKinetics' object validator
VectSimulateMultiLabel | Vectorized simulation of one replicate of multi-label NR-seq data
VisualizeDropout | Make plots to visually assess dropout trends