Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets

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Documentation for package ‘bakR’ version 1.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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