# Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets

## Documentation for package ‘bakR’ version 0.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

bakR-package | The 'bakR' package.
bakR | The 'bakR' package.
bakRData | bakR Data object helper function for users
bakRFit | Estimating kinetic parameters from nucleotide recoding RNA-seq data
cBprocess | Curate data in bakRData object for statistical modeling
cB_small | Example cB data frame
fast_analysis | Efficiently analyze nucleotide recoding data
FnPCA | Creating PCA plots with logit(fn) estimates
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
NSSHeat | Construct heatmap for non-steady state (NSS) analysis
NSSHeat2 | Construct heatmap for non-steady state (NSS) analysis with improved mechanism score
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.
reliableFeatures | Identify features (e.g., transcripts) with high quality data
Simulate_bakRData | Simulating nucleotide recoding data
TL_stan | Fit 'Stan' models to nucleotide recoding RNA-seq data analysis
validate_bakRData | bakR Data object validator