| annotatedGenome-class | Class "annotatedGenome" |
| asymmetryCheck | Plot asymmetry coefficients for the observed data and compare... |
| calcDenovo | Estimate expression of gene splicing variants de novo. |
| calcExp | Estimate expression of a known set of gene splicing variants. |
| denovoExpr | Estimate expression for de novo splicing variants. |
| denovoGeneExpr-class | Class "denovoGenomeExpr" |
| denovoGenomeExpr-class | Class "denovoGeneExpr" |
| distrsGSE37704 | Estimated read start and insert size distributions from MiSeq... |
| genePlot | Plot exon structure for each transcript of a given gene. |
| getDistrs | Compute fragment start and fragment length distributions |
| getIsland | getIsland returns the island id associated to a given entrez... |
| getNreads | Get total number of paths in each island from a pathCounts... |
| getReads | getReads returns the reads stored in a 'procBam' object. |
| getRoc | Operating characteristics of differential expression analysis |
| hg19DB | Subset of human genome (UCSC hg19 version) |
| K562.r1l1 | Toy RNA-seq data from RGASP project. |
| mergeBatches | Merge two ExpressionSet objects by doing quantile... |
| mergeExp | Merge splicing variant expression from multiple samples |
| modelPrior | Set prior distribution on expressed splicing variants. |
| modelPriorAS-class | Class "modelPriorAS" |
| pathCounts | Compute exon path counts |
| pathCounts-class | Class "pathCounts" |
| plotExpr | Plot inferred gene structure and expression. |
| plot-methods | Plot estimated read start and fragment length distributions. |
| plotPriorAS | Plot prior distribution on set of expressed variants (i.e.... |
| probNonEquiv | 'probNonEquiv' performs a Bayesian hypothesis test for... |
| procBam | Process BAM object |
| procBam-class | Class "procBam" |
| procGenome | Create an annotatedGenome object that stores information... |
| qqnormGenomeWide | Genome-wide qq-normal and qq-gamma plots |
| quantileNorm | Apply quantile normalization |
| relexprByGene | Compute relative expressions within each gene |
| rmShortInserts | Remove reads with short insert sizes from imported BAM files. |
| simMAE | Simulate Mean Absolute Error (MAE) in estimating isoform... |
| simMAEcheck | Model checking for One Sample Problems. |
| simMultSamples | Simulate paired end reads for multiple future samples based... |
| simReads | Function to simulate paired end reads following given read... |
| simulatedSamples-class | Class "simulatedSamples" |
| splitGenomeByLength | Split an annotatedGenome object into subsets according to... |
| subsetGenome | subsetGenome subsets an object of class annotatedGenome for a... |
| transcripts | Extracts transcript information (exon start and ends) from an... |
| txLength-methods | ~~ Methods for Function 'txLength' in Package 'casper' ~~ |
| wrapDenovo | Run all necessary steps to get expression estimates from... |
| wrapKnown | Run all necessary steps to get expression estimates from... |
