# Context-Aware Transcript Quantification from Long Read RNA-Seq data

## Documentation for package ‘bambu’ version 3.14.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

bambu | long read isoform reconstruction and quantification
compareTranscripts | compare alternatively-spliced transcripts
plotBambu | plot.bambu
prepareAnnotations | prepare reference annotations for long read RNA-Seq analysis with Bambu
readFromGTF | convert a GTF file into a GRangesList
trainBambu | Function to train a model for use on other data
transcriptToGeneExpression | transcript to gene expression
writeBambuOutput | Write Bambu results to GTF and transcript/gene-count files
writeToGTF | write GRangeslist into GTF file