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

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Documentation for package ‘EZbakR’ version 0.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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