CorrectDropout          Correcting for metabolic labeling induced RNA
                        dropout
DissectMechanism        Construct heatmap for non-steady state (NSS)
                        analysis with improved mechanism score
FnPCA                   Creating PCA plots with logit(fn) estimates
FnPCA2                  Creating PCA plots with logit(fn) estimates
GS_table                Example cB data frame
GSprocessing            Prep GRAND-SLAM output for 'bakRFnData'
Heatmap_kdeg            Creating a L2FC(kdeg) matrix that can be passed
                        to heatmap functions
NSSHeat                 Construct heatmap for non-steady state (NSS)
                        analysis
QC_checks               Check data quality and make suggestions to user
                        about what analyses to run.
QuantifyDropout         Fit dropout model to quantify dropout frequency
Simulate_bakRData       Simulating nucleotide recoding data
Simulate_relative_bakRData
                        Simulating nucleotide recoding data with
                        relative count data
TL_stan                 Fit 'Stan' models to nucleotide recoding
                        RNA-seq data analysis
VisualizeDropout        Visualize dropout
avg_and_regularize      Efficiently average replicates of nucleotide
                        recoding data and regularize
bakR-package            The 'bakR' package.
bakRData                bakR Data object helper function for users
bakRFit                 Estimating kinetic parameters from nucleotide
                        recoding RNA-seq data
bakRFnData              bakRFnData object helper function for users
cB_small                Example cB data frame
cBprocess               Curate data in bakRData object for statistical
                        modeling
fast_analysis           Efficiently analyze nucleotide recoding data
fn_process              Curate data in bakRFnData object for
                        statistical modeling
fns                     Example fraction news (fns) data frame
metadf                  Example meatdf data frame
new_bakRData            bakRData object constructor for internal use
new_bakRFnData          bakRFnData object constructor for internal use
plotMA                  Creating L2FC(kdeg) MA plot from fit objects
plotVolcano             Creating L2FC(kdeg) volcano plot from fit
                        objects
reliableFeatures        Identify features (e.g., transcripts) with high
                        quality data
validate_bakRData       bakR Data object validator
validate_bakRFnData     bakRFnData object validator
