R: Genome-Wide RNA Degradation Analysis Using BRIC-Seq Data

# Genome-Wide RNA Degradation Analysis Using BRIC-Seq Data

## Documentation for package ‘bridger2’ version 0.1.0

- DESCRIPTION file
- Package README

## Help Pages

BridgeRCore | BridgeR basic function for calculating RNA half-life from BRIC-seq data
BridgeRDatasetChecker | BRIC-seq Dataset checker
BridgeRDataSetFromMatrix | Calculate relative RPKM expression from data.table format.
BridgeRDataSetFromRaw | Calculate relative RPKM expression from raw data.
BridgeReport | Shinyapp reporting for drawing RNA decay curve.
BridgeRGrubbsTest | RNA half-life Grubbs test.
BridgeRHalfLifeCalc3models | Calculate RNA half-life for each gene using 3model method.
BridgeRHalfLifeCalcR2Select | Calculate RNA half-life for each gene using R2 selection method.
BridgeRNormalization | Calculate the normalized RPKM for BRIC-seq dataset.
BridgeRNormalizationFactors | Calculate normalization factors for BRIC-seq datasets.
BridgeRNormalizationFactorsHK | Calculate normalization factors from house-keeping genes.
BridgeRPvalueEvaluation | Calculate Fold-change of RNA half-life and p-value.
BridgeRResultChecker | BRIC-seq result checker
CalcHalflifeDeviation | Calculate RNA half-life SD.
halflife_table | BRIC-seq result dataset for p-value estimation using grubbs test
RNA_halflife_comparison | test BRIC-seq dataset for RNA half-life comparison
RNA_halflife_comparison_HK | test BRIC-seq dataset for RNA half-life comparison using House-keeping genes.
RNA_halflife_grubbs_test | test BRIC-seq dataset for p-value estimation using grubbs test