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.
• Package NEWS.

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