Genome-Wide RNA Degradation Analysis Using BRIC-Seq Data

Documentation for package ‘bridger2’ version 0.1.0

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