# Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets

## Documentation for package ‘bakR’ version 1.0.1

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

## Help Pages

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