| 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 |