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 |