Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets


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Documentation for package ‘bakR’ version 1.0.1

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