Package index • EZbakR

All functions

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.

DeconvolveFractions(): Deconvolve multi-feature fractions.

EZDynamics(): Generalized dynamical systems modeling

EZMAPlot(): Make an MAPlot from EZbakR comparison

EZQC(<EZbakRArrowData>): Run quality control checks

EZQC(<EZbakRData>): Run quality control checks

EZQC(<EZbakRFractions>): Run quality control checks

EZQC(): Run quality control checks

EZSimulate(): Simulate NR-seq data for multiple replicates of multiple biological conditions

EZVolcanoPlot(): Make a VolcanoPlot from EZbakR comparison

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

EZget(): Easily get EZbakR table of estimates of interest

EZpcaPlot(): Make an MAPlot from EZbakR comparison

EstimateFractions(): Estimate fractions of each RNA population.

EstimateIsoformFractions(): Estimate isoform-specific fraction news (or more generally "fractions").

EstimateKinetics(): Estimate kinetic parameters

EstimateMutRates(): Estimate mutation rates

ImportIsoformQuant(): Import transcript isoform quantification into EZbakRData object

NormalizeForDropout(): Normalize for experimental/bioinformatic dropout of labeled RNA.

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

VectSimulateMultiLabel(): Vectorized simulation of one replicate of multi-label NR-seq data

VisualizeDropout(): Make plots to visually assess dropout trends

create_fraction_design(): Generate a fraction_design table for EstimateFractions.

example_cB: Example cB table

example_metadf: Example metadf

get_normalized_read_counts(): Get normalized read counts from either a cB table or EZbakRFractions 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

ode_models: Example ODE model graphs and formulas

print(<EZbakRArrowData>): Print method for EZbakRArrowData objects

print(<EZbakRData>): Print method for EZbakRData objects

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