Transcript expression inference and differential expression analysis for RNA-seq data


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Documentation for package ‘BitSeq’ version 1.26.1

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BitSeq-package Bayesian Inference of Transcripts from Sequencing data
BitSeq Bayesian Inference of Transcripts from Sequencing data
estimateDE Estimate condition mean expression and calculate Probability of Positive Log Ratio(PPLR)
estimateExpression Estimate expression of transcripts
estimateExpressionLegacy Estimate expression of transcripts
estimateHyperPar Estimate hyperparameters for DE model using expression samples and joint mean expression
estimateVBExpression Estimate expression of transcripts using VB
getDE Estimate Probability of Positive Log Ratio
getExpression Estimate transcript expression
getGeneExpression Calculate gene expression or relative within gene expression
getMeanVariance Calculate mean and variance of expression samples
getWithinGeneExpression Calculate gene expression or relative within gene expression
loadSamples Loading and saving expression samples
parseAlignment Compute probabilities of alignments
tri.file.hasGeneNames Manage file containing information about transcript reference
tri.file.setGeneNames Manage file containing information about transcript reference
tri.hasGeneNames Manage information about transcript reference
tri.load Manage information about transcript reference
tri.save Manage information about transcript reference
tri.setGeneNames Manage information about transcript reference
writeSamples Loading and saving expression samples