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 |