| annotate_assembly | match assembled transcripts to annotated transcripts |
| ballgown-class | Ballgown |
| ballgown-constructor | constructor function for ballgown objects |
| ballgown-package | The ballgown package for analysis of transcript assemblies |
| ballgownrsem | load RSEM data into a ballgown object |
| bg | Toy ballgown object |
| checkAssembledTx | plot annotated and assembled transcripts together |
| clusterTranscripts | group a gene's assembled transcripts into clusters |
| collapseTranscripts | cluster a gene's transcripts and calculate cluster-level... |
| contains | determine if one set of GRanges fully contains any of another... |
| dirs | extract paths to tablemaker output |
| eexpr | extract exon-level expression measurements from ballgown... |
| expr | extract expression components from ballgown objects |
| exprfilter | subset ballgown objects using an expression filter |
| expr-replace | Replacement method for expr slot in ballgown objects |
| geneIDs | get gene IDs from a ballgown object |
| geneNames | get gene names from a ballgown object |
| getAttributeField | extract a specific field of the "attributes" column of a data... |
| getGenes | label assembled transcripts with gene names |
| gexpr | extract gene-level expression measurements from ballgown... |
| gffRead | read in GTF/GFF file as a data frame |
| gffReadGR | read in gtf file as GRanges object |
| iexpr | extract transcript-level expression measurements from... |
| indexes | extract the indexes from ballgown objects |
| indexes-replace | Replace method for indexes slot in ballgown objects |
| last | get the last element |
| mergedDate | extract package version & creation date from ballgown object |
| pctOverlap | calculate percent overlap between two GRanges objects |
| pData | extract phenotype data from a ballgown object |
| pData-replace | Replacement method for pData slot in ballgown objects |
| plotLatentTranscripts | cluster assembled transcripts and plot the results |
| plotMeans | visualize transcript abundance by group |
| plotTranscripts | visualize structure of assembled transcripts |
| sampleNames | get names of samples in a ballgown objects |
| seqnames | get sequence (chromosome) names from ballgown object |
| stattest | statistical tests for differential expression in ballgown |
| structure | extract structure components from ballgown objects |
| subset | subset ballgown objects to specific samples or genomic... |
| texpr | extract transcript-level expression measurements from... |
| tGene | Connect a transcript to its gene |
| transcriptIDs | get numeric transcript IDs from a ballgown object |
| transcriptNames | get transcript names from a ballgown object |
| writeFiles | write files to disk from ballgown object |
