Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets

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Documentation for package ‘bakR’ version 0.4.0

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