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.

EZDynamics(): Generalized dynamical systems modeling

EZMAPlot(): Make an MAPlot from EZbakR comparison

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

EstimateFractions(<EZbakRArrowData>): Estimate fractions of each RNA population using Apache Arrow backend.

EstimateFractions(<EZbakRData>): Estimate fractions of each RNA population with standard EZbakRData object

EstimateFractions(): Estimate fractions of each RNA population

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

EstimateKinetics(): Generic function for estimating kinetic parameters.

EstimateMutRates(<EZbakRArrowData>): Estimate mutation rates

EstimateMutRates(<EZbakRData>): Estimate mutation rates

EstimateMutRates(): Estimate mutation rates

ImportIsoformQuant(): Import transcript isoform quantification into EZbakRData object

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

create_fraction_design(): Generate a fraction_design table for EstimateFractions

example_cB: Example cB table

example_metadf: Example metadf

get_normalized_read_counts(<EZbakRFractions>): Get normalized read counts from either an EZbakRFractions object.

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

get_normalized_read_counts(<default>): Get normalized read counts from either a cB table in an 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

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