Package index • bakR

All functions

CorrectDropout(): Correcting for metabolic labeling induced RNA dropout

DissectMechanism(): Construct heatmap for non-steady state (NSS) analysis with improved mechanism score

FnPCA(): Creating PCA plots with logit(fn) estimates

FnPCA2(): Creating PCA plots with logit(fn) estimates

GS_table: Example cB data frame

GSprocessing(): Prep GRAND-SLAM output for bakRFnData

Heatmap_kdeg(): Creating a L2FC(kdeg) matrix that can be passed to heatmap functions

NSSHeat(): Construct heatmap for non-steady state (NSS) analysis

QC_checks(): Check data quality and make suggestions to user about what analyses to run.

QuantifyDropout(): Fit dropout model to quantify dropout frequency

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

VisualizeDropout(): Visualize dropout

avg_and_regularize(): Efficiently average replicates of nucleotide recoding data and regularize

bakR-package 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

cB_small: Example cB data frame

cBprocess(): Curate data in bakRData object for statistical modeling

fast_analysis(): Efficiently analyze nucleotide recoding data

fn_process(): Curate data in bakRFnData object for statistical modeling

fns: Example fraction news (fns) data frame

metadf: Example meatdf data frame

new_bakRData(): bakRData object constructor for internal use

new_bakRFnData(): bakRFnData object constructor for internal use

plotMA(): Creating L2FC(kdeg) MA plot from fit objects

plotVolcano(): Creating L2FC(kdeg) volcano plot from fit objects

reliableFeatures(): Identify features (e.g., transcripts) with high quality data

validate_bakRData(): bakR Data object validator

validate_bakRFnData(): bakRFnData object validator