Man pages for bakR
Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets
| avg_and_regularize | Efficiently average replicates of nucleotide recoding data... |
| bakRData | bakR Data object helper function for users |
| bakRFit | Estimating kinetic parameters from nucleotide recoding... |
| bakRFnData | bakRFnData object helper function for users |
| bakR-package | The 'bakR' package. |
| 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... |
| fast_analysis | Efficiently analyze nucleotide recoding data |
| FnPCA | Creating PCA plots with logit(fn) estimates |
| FnPCA2 | Creating PCA plots with logit(fn) estimates |
| fn_process | Curate data in bakRFnData object for statistical modeling |
| fns | Example fraction news (fns) data frame |
| 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... |
| 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... |
| 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... |
| validate_bakRData | bakR Data object validator |
| validate_bakRFnData | bakRFnData object validator |
| VisualizeDropout | Visualize dropout |
